Binding Site Information of Target

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Target General Information
Drug Binding Sites of Target
References
Target General Information  Top
Target ID T34296 Target Info
Target Name Matrix metalloproteinase-13 (MMP-13)
Synonyms Matrix metalloproteinase 13; Collagenase-3; Collagenase 3
Target Type Clinical trial Target
Gene Name MMP13
Biochemical Class Peptidase
UniProt ID
MMP13_HUMAN
Drug Binding Sites of Target  Top
Ligand Name: Acetohydroxamic acid Ligand Info
Structure Description Crystal structure analysis of the MMP13 catalytic domain in complex with specific inhibitor PDB:2OW9
Method X-ray diffraction Resolution 1.74 Å Mutation No [1]
PDB Sequence
YNVFPRTLKW
92
SKMNLTYRIV
102
NYTPDMTHSE
112
VEKAFKKAFK
122
VWSDVTPLNF
132

TRLHDGIADI
142
MISFGIKEHG
152
DFYPFDGPSG
162
LLAHAFPPGP
172
NYGGDAHFDD
182

DETWTSSSKG
192
YNLFLVAAHE
202
FGHSLGLDHS
212
KDPGALMFPI
222
YTYTGKSHFM
232

LPDDDVQGIQ
242
SLYGPGD
Residue
Distance (Å)
LEU163
3.862
ALA165
2.869
HIS166
3.820
HIS201
3.088
Residue
Distance (Å)
GLU202
2.513
HIS205
3.135
HIS211
2.818
Click to View More Binding Site Information of This Target and Ligand Pair
Ligand Name: PMID17935984C1 Ligand Info
Structure Description Crystal structure of the catalytic domain of MMP-13 complexed with a potent pyrimidinetrione inhibitor PDB:1YOU
Method X-ray diffraction Resolution 2.30 Å Mutation No [2]
PDB Sequence
YNVFPRTLKW
113
SKMNLTYRIV
123
NYTPDMTHSE
133
VEKAFKKAFK
143
VWSDVTPLNF
153

TRLHDGIADI
163
MISFGIKEHG
173
DFYPFDGPSG
183
LLAHAFPPGP
193
NYGGDAHFDD
203

DETWTSSSKG
213
YNLFLVAAHE
223
FGHSLGLDHS
233
KDPGALMFPI
243
YTYTGKSHFM
253

LPDDDVQGIQ
263
SLYGPGDE
Residue
Distance (Å)
GLY183
4.517
LEU184
3.502
LEU185
2.823
ALA186
2.430
HIS187
3.784
ALA188
4.513
LEU218
4.021
VAL219
3.770
HIS222
3.309
GLU223
2.740
Residue
Distance (Å)
HIS226
3.423
HIS232
3.537
ALA238
4.374
LEU239
3.121
PHE241
3.114
PRO242
3.529
ILE243
3.276
TYR244
3.554
THR245
3.583
Ligand Name: 1-Methyloxy-4-Sulfone-Benzene Ligand Info
Structure Description SOLUTION STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN COLLAGENASE-3 (MMP-13) COMPLEXED TO A POTENT NON-PEPTIDIC SULFONAMIDE INHIBITOR PDB:1EUB
Method Solution NMR Resolution N.A. Mutation No [3]
PDB Sequence
YNVFPRTLKW
113
SKMNLTYRIV
123
NYTPDMTHSE
133
VEKAFKKAFK
143
VWSDVTPLNF
153

TRLHDGIADI
163
MISFGIKEHG
173
DFYPFDGPSG
183
LLAHAFPPGP
193
NYGGDAHFDD
203

DETWTSSSKG
213
YNLFLVAAHE
223
FGHSLGLDHS
233
KDPGALMFPI
243
YTYTGKSHFM
253

LPDDDVQGIQ
263
SLYGPGDEDP
273
N
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .MSB or .MSB2 or .MSB3 or :3MSB;style chemicals stick;color identity;select .A:183 or .A:184 or .A:185 or .A:186 or .A:201 or .A:214 or .A:218 or .A:219 or .A:222 or .A:223 or .A:239 or .A:241 or .A:242 or .A:243 or .A:244 or .A:246; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
GLY183
4.974
LEU184
4.072
LEU185
2.049
ALA186
1.812
PHE201
4.344
TYR214
4.123
LEU218
1.873
VAL219
2.356
Residue
Distance (Å)
HIS222
1.895
GLU223
3.853
LEU239
2.508
PHE241
2.993
PRO242
2.342
ILE243
2.645
TYR244
1.889
TYR246
4.918
Ligand Name: 3-Methylpyridine Ligand Info
Structure Description SOLUTION STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN COLLAGENASE-3 (MMP-13) COMPLEXED TO A POTENT NON-PEPTIDIC SULFONAMIDE INHIBITOR PDB:1EUB
Method Solution NMR Resolution N.A. Mutation No [3]
PDB Sequence
YNVFPRTLKW
113
SKMNLTYRIV
123
NYTPDMTHSE
133
VEKAFKKAFK
143
VWSDVTPLNF
153

TRLHDGIADI
163
MISFGIKEHG
173
DFYPFDGPSG
183
LLAHAFPPGP
193
NYGGDAHFDD
203

DETWTSSSKG
213
YNLFLVAAHE
223
FGHSLGLDHS
233
KDPGALMFPI
243
YTYTGKSHFM
253

LPDDDVQGIQ
263
SLYGPGDEDP
273
N
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .3MP or .3MP2 or .3MP3 or :33MP;style chemicals stick;color identity;select .A:182 or .A:183 or .A:184 or .A:185 or .A:186 or .A:222 or .A:232 or .A:240 or .A:241 or .A:242 or .A:243; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
SER182
4.717
GLY183
1.980
LEU184
3.296
LEU185
3.312
ALA186
4.762
HIS222
4.512
Residue
Distance (Å)
HIS232
4.139
MET240
4.160
PHE241
3.886
PRO242
1.851
ILE243
4.656
Ligand Name: Hydroxyaminovaline Ligand Info
Structure Description SOLUTION STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN COLLAGENASE-3 (MMP-13) COMPLEXED TO A POTENT NON-PEPTIDIC SULFONAMIDE INHIBITOR PDB:1EUB
Method Solution NMR Resolution N.A. Mutation No [3]
PDB Sequence
YNVFPRTLKW
113
SKMNLTYRIV
123
NYTPDMTHSE
133
VEKAFKKAFK
143
VWSDVTPLNF
153

TRLHDGIADI
163
MISFGIKEHG
173
DFYPFDGPSG
183
LLAHAFPPGP
193
NYGGDAHFDD
203

DETWTSSSKG
213
YNLFLVAAHE
223
FGHSLGLDHS
233
KDPGALMFPI
243
YTYTGKSHFM
253

LPDDDVQGIQ
263
SLYGPGDEDP
273
N
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set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .HAV or .HAV2 or .HAV3 or :3HAV;style chemicals stick;color identity;select .A:183 or .A:184 or .A:185 or .A:186 or .A:187 or .A:188 or .A:201 or .A:222 or .A:223 or .A:226 or .A:232 or .A:240 or .A:241 or .A:242; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
GLY183
3.221
LEU184
1.924
LEU185
2.509
ALA186
2.031
HIS187
3.066
ALA188
4.202
PHE201
4.994
Residue
Distance (Å)
HIS222
2.098
GLU223
2.516
HIS226
2.143
HIS232
2.772
MET240
3.592
PHE241
4.729
PRO242
3.785
Ligand Name: PMID22017539C15 Ligand Info
Structure Description X-RAY Co-structure of MMP-13 with 4-[({5-[2-(ethoxycarbonyl)-1H-indol-5-yl]-1-methyl-1H-pyrazol-3-yl}formamido)methyl]benzoate PDB:5BPA
Method X-ray diffraction Resolution 1.79 Å Mutation No [4]
PDB Sequence
YNVFPRTLKW
113
SKMNLTYRIV
123
NYTPDMTHSE
133
VEKAFKKAFK
143
VWSDVTPLNF
153

TRLHDGIADI
163
MISFGIKEHG
173
DFYPFDGPSG
183
LLAHAFPPGP
193
NYGGDAHFDD
203

DETWTSSSKG
213
YNLFLVAAHE
223
FGHSLGLDHS
233
KDPGALMFPI
243
YTYTGKSHFM
253

LPDDDVQGIQ
263
SLYGPGDED
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set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .4UF or .4UF2 or .4UF3 or :34UF;style chemicals stick;color identity;select .A:140 or .A:185 or .A:209 or .A:215 or .A:217 or .A:218 or .A:219 or .A:222 or .A:223 or .A:237 or .A:238 or .A:239 or .A:240 or .A:241 or .A:242 or .A:243 or .A:244 or .A:245 or .A:246 or .A:247 or .A:248 or .A:249 or .A:250 or .A:251 or .A:252 or .A:253 or .A:255; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
LYS140
2.726
LEU185
3.392
SER209
4.134
ASN215
3.345
PHE217
3.596
LEU218
3.602
VAL219
4.076
HIS222
3.139
GLU223
3.611
GLY237
4.648
ALA238
3.307
LEU239
3.250
MET240
4.982
PHE241
2.768
Residue
Distance (Å)
PRO242
3.645
ILE243
3.214
TYR244
3.870
THR245
3.210
TYR246
3.509
THR247
2.793
GLY248
4.444
LYS249
3.617
SER250
4.123
HIS251
3.914
PHE252
3.494
MET253
4.910
PRO255
3.890
Ligand Name: RS-130830 Ligand Info
Structure Description COLLAGENASE-3 (MMP-13) COMPLEXED TO A SULPHONE-BASED HYDROXAMIC ACID PDB:830C
Method X-ray diffraction Resolution 1.60 Å Mutation No [5]
PDB Sequence
YNVFPRTLKW
113
SKMNLTYRIV
123
NYTPDMTHSE
133
VEKAFKKAFK
143
VWSDVTPLNF
153

TRLHDGIADI
163
MISFGIKEHG
173
DFYPFDGPSG
183
LLAHAFPPGP
193
NYGGDAHFDD
203

DETWTSSSKG
213
YNLFLVAAHE
223
FGHSLGLDHS
233
KDPGALMFPI
243
YTYTFMLPDD
257

DVQGIQSLYG
267
PGDE
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set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .RS1 or .RS12 or .RS13 or :3RS1;style chemicals stick;color identity;select .A:183 or .A:184 or .A:185 or .A:186 or .A:187 or .A:188 or .A:218 or .A:219 or .A:222 or .A:223 or .A:226 or .A:232 or .A:238 or .A:239 or .A:240 or .A:241 or .A:242 or .A:243 or .A:244 or .A:245; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
GLY183
3.938
LEU184
2.993
LEU185
1.903
ALA186
2.236
HIS187
3.564
ALA188
3.688
LEU218
3.216
VAL219
3.039
HIS222
2.547
GLU223
1.983
Residue
Distance (Å)
HIS226
2.749
HIS232
2.662
ALA238
3.577
LEU239
2.781
MET240
4.489
PHE241
2.532
PRO242
2.839
ILE243
2.934
TYR244
2.654
THR245
2.976
Ligand Name: WAY-151693 Ligand Info
Structure Description SOLUTION STRUCTURE OF THE CATALYTIC FRAGMENT OF HUMAN COLLAGENASE-3 (MMP-13) COMPLEXED WITH A HYDROXAMIC ACID INHIBITOR PDB:1FLS
Method Solution NMR Resolution N.A. Mutation No [6]
PDB Sequence
TLKWSKMNLT
16
YRIVNYTPDM
26
THSEVEKAFK
36
KAFKVWSDVT
46
PLNFTRLHDG
56

IADIMISFGI
66
KEHGDFYPFD
76
GPSGLLAHAF
86
PPGPNYGGDA
96
HFDDDETWTS
106

SSKGYNLFLV
116
AAHEFGHSLG
126
LDHSKDPGAL
136
MFPIYTYTGK
146
SHFMLPDDDV
156

QGIQSLYG
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set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .WAY or .WAY2 or .WAY3 or :3WAY;style chemicals stick;color identity;select .A:80 or .A:81 or .A:82 or .A:83 or .A:84 or .A:115 or .A:116 or .A:119 or .A:120 or .A:123 or .A:129 or .A:136 or .A:138 or .A:139 or .A:140 or .A:141 or .A:142; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
GLY80
2.774
LEU81
2.534
LEU82
2.592
ALA83
3.330
HIS84
3.910
LEU115
2.609
VAL116
2.576
HIS119
2.435
GLU120
4.146
Residue
Distance (Å)
HIS123
3.084
HIS129
2.609
LEU136
3.954
PHE138
3.938
PRO139
2.710
ILE140
2.918
TYR141
1.889
THR142
3.588
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Ligand Name: N-[(2s)-4-(5-Fluoropyrimidin-2-Yl)-1-({4-[5-(2,2,2-Trifluoroethoxy)pyrimidin-2-Yl]piperazin-1-Yl}sulfonyl)butan-2-Yl]-N-Hydroxyformamide Ligand Info
Structure Description Mmp13 in complex with a reverse hydroxamate Zn-binder PDB:4JP4
Method X-ray diffraction Resolution 1.43 Å Mutation No [7]
PDB Sequence
YNVFPRTLKW
113
SKMNLTYRIV
123
NYTPDMTHSE
133
VEKAFKKAFK
143
VWSDVTPLNF
153

TRLHDGIADI
163
MISFGIKEHG
173
DFYPFDGPSG
183
LLAHAFPPGP
193
NYGGDAHFDD
203

DETWTSSSKG
213
YNLFLVAAHE
223
FGHSLGLDHS
233
KDPGALMFPI
243
YTYHFMLPDD
257

DVQGIQSLYG
267
PGDED
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set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .AZ4 or .AZ42 or .AZ43 or :3AZ4;style chemicals stick;color identity;select .A:183 or .A:184 or .A:185 or .A:186 or .A:187 or .A:188 or .A:218 or .A:219 or .A:222 or .A:223 or .A:226 or .A:230 or .A:231 or .A:232 or .A:237 or .A:238 or .A:239 or .A:241 or .A:242 or .A:243 or .A:244 or .A:245 or .A:252; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
GLY183
3.728
LEU184
3.683
LEU185
2.877
ALA186
3.210
HIS187
3.603
ALA188
3.268
LEU218
3.586
VAL219
3.915
HIS222
3.068
GLU223
2.572
HIS226
3.042
LEU230
4.791
Residue
Distance (Å)
ASP231
4.082
HIS232
2.758
GLY237
4.397
ALA238
3.776
LEU239
3.244
PHE241
3.324
PRO242
3.132
ILE243
3.498
TYR244
3.542
THR245
3.070
PHE252
3.622
Ligand Name: 3-[({2-[4-({[(4s)-4-Methyl-2,5-Dioxoimidazolidin-4-Yl]methyl}sulfonyl)piperazin-1-Yl]pyrimidin-5-Yl}oxy)methyl]benzonitrile Ligand Info
Structure Description Mmp13 in complex with a piperazine hydantoin ligand PDB:4JPA
Method X-ray diffraction Resolution 2.00 Å Mutation No [7]
PDB Sequence
YNVFPRTLKW
113
SKMNLTYRIV
123
NYTPDMTHSE
133
VEKAFKKAFK
143
VWSDVTPLNF
153

TRLHDGIADI
163
MISFGIKEHG
173
DFYPFDGPSG
183
LLAHAFPPGP
193
NYGGDAHFDD
203

DETWTSSSKG
213
YNLFLVAAHE
223
FGHSLGLDHS
233
KDPGALMFPI
243
YTYHFMLPDD
257

DVQGIQSLYG
267
PGDED
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set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .AZ6 or .AZ62 or .AZ63 or :3AZ6;style chemicals stick;color identity;select .A:183 or .A:184 or .A:185 or .A:186 or .A:187 or .A:188 or .A:218 or .A:219 or .A:222 or .A:223 or .A:226 or .A:232 or .A:237 or .A:238 or .A:239 or .A:241 or .A:242 or .A:243 or .A:244 or .A:245 or .A:246 or .A:252 or .A:255; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
GLY183
3.806
LEU184
3.619
LEU185
3.042
ALA186
2.818
HIS187
3.692
ALA188
4.484
LEU218
3.593
VAL219
4.060
HIS222
3.407
GLU223
2.774
HIS226
3.454
HIS232
3.116
Residue
Distance (Å)
GLY237
3.616
ALA238
3.612
LEU239
3.379
PHE241
3.232
PRO242
3.614
ILE243
3.024
TYR244
3.583
THR245
3.309
TYR246
3.242
PHE252
3.815
PRO255
4.133
Ligand Name: N-Phenyl-4-[(4h-1,2,4-Triazol-3-Ylsulfanyl)methyl]-1,3-Thiazol-2-Amine Ligand Info
Structure Description Crystal structure of the catalytic domain of MMP-13 complexed with N-phenyl-4-((4H-1,2,4-triazol-3-ylsulfanyl)methyl)-1,3-thiazol-2-amine PDB:5B5O
Method X-ray diffraction Resolution 1.20 Å Mutation No [8]
PDB Sequence
YNVFPRTLKW
113
SKMNLTYRIV
123
NYTPDMTHSE
133
VEKAFKKAFK
143
VWSDVTPLNF
153

TRLHDGIADI
163
MISFGIKEHG
173
DFYPFDGPSG
183
LLAHAFPPGP
193
NYGGDAHFDD
203

DETWTSSSKG
213
YNLFLVAAHE
223
FGHSLGLDHS
233
KDPGALMFPI
243
YTYTGFMLPD
256

DDVQGIQSLY
266
GPGDEDP
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set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .WMM or .WMM2 or .WMM3 or :3WMM;style chemicals stick;color identity;select .A:185 or .A:186 or .A:187 or .A:218 or .A:219 or .A:222 or .A:223 or .A:226 or .A:232 or .A:238 or .A:239 or .A:241 or .A:242 or .A:243 or .A:244 or .A:245; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
LEU185
4.438
ALA186
2.897
HIS187
4.039
LEU218
3.423
VAL219
4.128
HIS222
3.298
GLU223
3.148
HIS226
3.528
Residue
Distance (Å)
HIS232
3.143
ALA238
4.474
LEU239
3.296
PHE241
2.831
PRO242
3.136
ILE243
3.307
TYR244
3.676
THR245
3.789
Ligand Name: (S)-3-Methyl-2-(4'-(((4-Oxo-4,5,6,7-Tetrahydro-3h-Cyclopenta[d]pyrimidin-2-Yl)thio)methyl)-[1,1'-Biphenyl]-4-Ylsulfonamido)butanoic Acid Ligand Info
Structure Description Matrix metalloproteinase-13 complexed with selective inhibitor compound (S)-10a PDB:5UWK
Method X-ray diffraction Resolution 1.60 Å Mutation No [9]
PDB Sequence
FPRTLKWSKM
116
NLTYRIVNYT
126
PDMTHSEVEK
136
AFKKAFKVWS
146
DVTPLNFTRL
156

HDGIADIMIS
166
FGIKEHGDFY
176
PFDGPSGLLA
186
HAFPPGPNYG
196
GDAHFDDDET
206

WTSSSKGYNL
216
FLVAAHEFGH
226
SLGLDHSKDP
236
GALMFPIYTY
246
TGFMLPDDDV
259

QGIQSLYGPG
269
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set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .8OM or .8OM2 or .8OM3 or :38OM;style chemicals stick;color identity;select .A:183 or .A:184 or .A:185 or .A:186 or .A:187 or .A:218 or .A:219 or .A:222 or .A:223 or .A:226 or .A:232 or .A:237 or .A:238 or .A:239 or .A:241 or .A:242 or .A:243 or .A:244 or .A:245 or .A:246 or .A:247 or .A:248 or .A:252 or .A:253 or .A:255; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
GLY183
4.744
LEU184
3.548
LEU185
2.777
ALA186
2.800
HIS187
4.305
LEU218
3.581
VAL219
3.990
HIS222
3.348
GLU223
2.712
HIS226
3.500
HIS232
2.953
GLY237
3.594
ALA238
3.884
Residue
Distance (Å)
LEU239
3.283
PHE241
3.137
PRO242
3.297
ILE243
3.559
TYR244
3.668
THR245
2.635
TYR246
3.922
THR247
2.408
GLY248
4.587
PHE252
3.661
MET253
4.622
PRO255
3.686
Ligand Name: 4-Oxo-N-{3-[2-(1h-1,2,4-Triazol-3-Ylsulfanyl)ethoxy]benzyl}-3,4-Dihydroquinazoline-2-Carboxamide Ligand Info
Structure Description Crystal structure of the catalytic domain of MMP-13 complexed with 4-oxo-N-(3-(2-(1H-1,2,4-triazol-3-ylsulfanyl)ethoxy)benzyl)-3,4-dihydroquinazoline-2-carboxamide PDB:5B5P
Method X-ray diffraction Resolution 1.60 Å Mutation No [8]
PDB Sequence
YNVFPRTLKW
113
SKMNLTYRIV
123
NYTPDMTHSE
133
VEKAFKKAFK
143
VWSDVTPLNF
153

TRLHDGIADI
163
MISFGIKEHG
173
DFYPFDGPSG
183
LLAHAFPPGP
193
NYGGDAHFDD
203

DETWTSSSKG
213
YNLFLVAAHE
223
FGHSLGLDHS
233
KDPGALMFPI
243
YTYTGHFMLP
255

DDDVQGIQSL
265
YGPGDED
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .WNN or .WNN2 or .WNN3 or :3WNN;style chemicals stick;color identity;select .A:185 or .A:186 or .A:187 or .A:218 or .A:219 or .A:222 or .A:223 or .A:226 or .A:232 or .A:237 or .A:238 or .A:239 or .A:240 or .A:241 or .A:242 or .A:243 or .A:244 or .A:245 or .A:246 or .A:247 or .A:248 or .A:252 or .A:253 or .A:255; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
LEU185
3.881
ALA186
3.020
HIS187
4.142
LEU218
3.422
VAL219
4.027
HIS222
2.944
GLU223
2.976
HIS226
3.127
HIS232
3.048
GLY237
4.181
ALA238
3.312
LEU239
3.122
Residue
Distance (Å)
MET240
4.904
PHE241
3.169
PRO242
3.101
ILE243
3.512
TYR244
3.493
THR245
2.719
TYR246
4.007
THR247
2.731
GLY248
4.409
PHE252
3.537
MET253
3.652
PRO255
3.720
Ligand Name: (R)-N-(3-Methyl-1-(Methylamino)-1-Oxobutan-2-Yl)-5-(4-(((4-Oxo-4,5,6,7-Tetrahydro-3h-Cyclopenta[d]pyrimidin-2-Yl)thio)methyl)phenyl)furan-2-Carboxamide Ligand Info
Structure Description Matrix metalloproteinase-13 complexed with selective inhibitor compound (R)-17a PDB:5UWM
Method X-ray diffraction Resolution 1.62 Å Mutation No [9]
PDB Sequence
> Chain A
LKWSKMNLTY
120
RIVNYTPDMT
130
HSEVEKAFKK
140
AFKVWSDVTP
150
LNFTRLHDGI
160

ADIMISFGIK
170
EHGDFYPFDG
180
PSGLLAHAFP
190
PGPNYGGDAH
200
FDDDETWTSS
210

SKGYNLFLVA
220
AHEFGHSLGL
230
DHSKDPGALM
240
FPIYTYTHFM
253
LPDDDVQGIQ
263

SLYGP
> Chain C
VTPLN
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .8OA or .8OA2 or .8OA3 or :38OA;style chemicals stick;color identity;select .A:183 or .A:184 or .A:185 or .A:186 or .A:218 or .A:219 or .A:222 or .A:223 or .A:237 or .A:238 or .A:239 or .A:241 or .A:242 or .A:243 or .A:244 or .A:245 or .A:246 or .A:247 or .A:252 or .A:253 or .A:255 or .C:215; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
GLY183[A]
3.461
LEU184[A]
3.450
LEU185[A]
2.805
ALA186[A]
3.721
LEU218[A]
3.705
VAL219[A]
3.922
HIS222[A]
3.269
GLU223[A]
3.107
GLY237[A]
3.846
ALA238[A]
4.264
LEU239[A]
3.191
Residue
Distance (Å)
PHE241[A]
3.150
PRO242[A]
3.622
ILE243[A]
3.447
TYR244[A]
3.640
THR245[A]
2.865
TYR246[A]
3.998
THR247[A]
2.918
PHE252[A]
3.703
MET253[A]
4.137
PRO255[A]
3.506
ASN215[C]
3.306
Ligand Name: (S)-N-(3-Methyl-1-(Methylamino)-1-Oxobutan-2-Yl)-5-(4-(((4-Oxo-4,5,6,7-Tetrahydro-3h-Cyclopenta[d]pyrimidin-2-Yl)thio)methyl)phenyl)furan-2-Carboxamide Ligand Info
Structure Description Matrix metalloproteinase-13 complexed with selective inhibitor compound (S)-17a PDB:5UWL
Method X-ray diffraction Resolution 2.55 Å Mutation No [9]
PDB Sequence
TLKWSKMNLT
119
YRIVNYTPDM
129
THSEVEKAFK
139
KAFKVWSDVT
149
PLNFTRLHDG
159

IADIMISFGI
169
KEHGDFYPFD
179
GPSGLLAHAF
189
PPGPNYGGDA
199
HFDDDETWTS
209

SSKGYNLFLV
219
AAHEFGHSLG
229
LDHSKDPGAL
239
MFPIYTYTGK
249
SHFMLPDDDV
259

QGIQSLYGPG
269
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .8OJ or .8OJ2 or .8OJ3 or :38OJ;style chemicals stick;color identity;select .A:182 or .A:183 or .A:184 or .A:185 or .A:186 or .A:214 or .A:218 or .A:219 or .A:222 or .A:223 or .A:237 or .A:238 or .A:239 or .A:241 or .A:242 or .A:243 or .A:244 or .A:245 or .A:246 or .A:247 or .A:248 or .A:252 or .A:253 or .A:255; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
SER182
4.012
GLY183
2.987
LEU184
3.362
LEU185
3.012
ALA186
3.769
TYR214
3.186
LEU218
3.678
VAL219
3.949
HIS222
3.431
GLU223
3.351
GLY237
4.305
ALA238
4.588
Residue
Distance (Å)
LEU239
3.336
PHE241
2.991
PRO242
3.080
ILE243
3.399
TYR244
3.130
THR245
2.787
TYR246
4.098
THR247
2.984
GLY248
4.536
PHE252
3.894
MET253
4.030
PRO255
3.630
Ligand Name: N-(2-aminoethyl)-4'-{[(4-oxo-4,5,6,7-tetrahydro-3H-cyclopenta[d]pyrimidin-2-yl)sulfanyl]methyl}[1,1'-biphenyl]-4-sulfonamide Ligand Info
Structure Description Matrix metalloproteinase-13 complexed with selective inhibitor compound 10d PDB:5UWN
Method X-ray diffraction Resolution 3.20 Å Mutation No [9]
PDB Sequence
RTLKWSKMNL
118
TYRIVNYTPD
128
MTHSEVEKAF
138
KKAFKVWSDV
148
TPLNFTRLHD
158

GIADIMISFG
168
IKEHGDFYPF
178
DGPSGLLAHA
188
FPPGPNYGGD
198
AHFDDDETWT
208

SSSKGYNLFL
218
VAAHEFGHSL
228
GLDHSKDPGA
238
LMFPIYTYTG
248
KSHFMLPDDD
258

VQGIQSLYGP
268
G
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .8O7 or .8O72 or .8O73 or :38O7;style chemicals stick;color identity;select .A:183 or .A:184 or .A:185 or .A:186 or .A:218 or .A:219 or .A:222 or .A:223 or .A:232 or .A:237 or .A:238 or .A:239 or .A:241 or .A:242 or .A:243 or .A:244 or .A:245 or .A:246 or .A:247 or .A:248 or .A:249 or .A:252 or .A:253 or .A:255; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
GLY183
3.911
LEU184
3.430
LEU185
3.107
ALA186
3.152
LEU218
3.690
VAL219
3.968
HIS222
3.320
GLU223
3.480
HIS232
4.528
GLY237
4.054
ALA238
3.737
LEU239
3.424
Residue
Distance (Å)
PHE241
3.176
PRO242
3.267
ILE243
3.392
TYR244
3.436
THR245
2.828
TYR246
3.906
THR247
2.320
GLY248
4.816
LYS249
3.675
PHE252
3.902
MET253
4.235
PRO255
3.799
Ligand Name: N-Hydroxy-N^2^-(3-Methylbutyl)-N^2^-(Naphthalen-2-Ylsulfonyl)-D-Valinamide Ligand Info
Structure Description MMP-13 complexed with 2-Napthylsulfonamide hydroxamic acid inhibitor PDB:3ZXH
Method X-ray diffraction Resolution 1.30 Å Mutation No [10]
PDB Sequence
YNVFPRTLKW
113
SKMNLTYRIV
123
NYTPDMTHSE
133
VEKAFKKAFK
143
VWSDVTPLNF
153

TRLHDGIADI
163
MISFGIKEHG
173
DFYPFDGPSG
183
LLAHAFPPGP
193
NYGGDAHFDD
203

DETWTSSSKG
213
YNLFLVAAHE
223
FGHSLGLDHS
233
KDPGALMFPI
243
YTYTGFMLPD
256

DDVQGIQSLY
266
GPGDED
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .E41 or .E412 or .E413 or :3E41;style chemicals stick;color identity;select .A:183 or .A:184 or .A:185 or .A:186 or .A:187 or .A:188 or .A:218 or .A:219 or .A:222 or .A:223 or .A:226 or .A:232 or .A:239 or .A:241 or .A:242 or .A:243 or .A:244 or .A:245; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
GLY183
4.061
LEU184
2.796
LEU185
1.972
ALA186
2.787
HIS187
3.080
ALA188
4.403
LEU218
4.779
VAL219
2.991
HIS222
3.030
Residue
Distance (Å)
GLU223
2.535
HIS226
2.762
HIS232
2.476
LEU239
4.657
PHE241
3.984
PRO242
3.043
ILE243
3.581
TYR244
2.987
THR245
4.846
Ligand Name: N-(3-Methoxybenzyl)-4-Oxo-3,4-Dihydrothieno[2,3-D]pyrimidine-2-Carboxamide Ligand Info
Structure Description Crystal structure of the catalytic domain of MMP-13 complexed with N-(3-methoxybenzyl)-4-oxo-3,4-dihydrothieno[2,3-d]pyrimidine-2-carboxamide PDB:3WV3
Method X-ray diffraction Resolution 1.60 Å Mutation No [11]
PDB Sequence
YNVFPRTLKW
113
SKMNLTYRIV
123
NYTPDMTHSE
133
VEKAFKKAFK
143
VWSDVTPLNF
153

TRLHDGIADI
163
MISFGIKEHG
173
DFYPFDGPSG
183
LLAHAFPPGP
193
NYGGDAHFDD
203

DETWTSSSKG
213
YNLFLVAAHE
223
FGHSLGLDHS
233
KDPGALMFPI
243
YTYKSHFMLP
255

DDDVQGIQSL
265
YGPGDEDP
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .WLL or .WLL2 or .WLL3 or :3WLL;style chemicals stick;color identity;select .A:185 or .A:218 or .A:219 or .A:222 or .A:223 or .A:237 or .A:238 or .A:239 or .A:240 or .A:241 or .A:242 or .A:243 or .A:244 or .A:245 or .A:246 or .A:252 or .A:253 or .A:255; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
LEU185
3.791
LEU218
3.696
VAL219
3.791
HIS222
3.293
GLU223
3.717
GLY237
4.119
ALA238
3.441
LEU239
3.045
MET240
4.856
Residue
Distance (Å)
PHE241
3.191
PRO242
3.926
ILE243
3.424
TYR244
3.427
THR245
2.768
TYR246
3.697
PHE252
3.408
MET253
3.692
PRO255
3.554
Ligand Name: 2-[(4-Methylbenzyl)sulfanyl]-3,5,6,7-Tetrahydro-4h-Cyclopenta[d]pyrimidin-4-One Ligand Info
Structure Description Matrix metalloproteinase-13 complexed with selective inhibitor compound Q1 PDB:4L19
Method X-ray diffraction Resolution 1.66 Å Mutation No [12]
PDB Sequence
YNVFPRTLKW
113
SKMNLTYRIV
123
NYTPDMTHSE
133
VEKAFKKAFK
143
VWSDVTPLNF
153

TRLHDGIADI
163
MISFGIKEHG
173
DFYPFDGPSG
183
LLAHAFPPGP
193
NYGGDAHFDD
203

DETWTSSSKG
213
YNLFLVAAHE
223
FGHSLGLDHS
233
KDPGALMFPI
243
YTYTGKSHFM
253

LPDDDVQGIQ
263
SLYGPG
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .1UA or .1UA2 or .1UA3 or :31UA;style chemicals stick;color identity;select .A:176 or .A:185 or .A:187 or .A:188 or .A:189 or .A:190 or .A:218 or .A:219 or .A:222 or .A:223 or .A:226 or .A:232 or .A:237 or .A:238 or .A:239 or .A:241 or .A:242 or .A:243 or .A:244 or .A:245 or .A:246 or .A:247 or .A:252 or .A:253 or .A:255; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
TYR176
3.211
LEU185
4.359
HIS187
4.342
ALA188
3.001
PHE189
3.200
PRO190
4.144
LEU218
3.587
VAL219
4.002
HIS222
3.449
GLU223
4.189
HIS226
3.592
HIS232
4.925
GLY237
3.766
Residue
Distance (Å)
ALA238
4.117
LEU239
3.290
PHE241
2.955
PRO242
3.704
ILE243
3.560
TYR244
3.823
THR245
2.745
TYR246
4.071
THR247
3.079
PHE252
3.275
MET253
4.239
PRO255
3.827
Ligand Name: 4-(4-{[(3s)-3-Hydroxy-1-Azabicyclo[2.2.2]oct-3-Yl]ethynyl}phenoxy)-N-(Pyridin-4-Ylmethyl)benzamide Ligand Info
Structure Description MMP13 in complex with a novel selective non zinc binding inhibitor PDB:2YIG
Method X-ray diffraction Resolution 1.70 Å Mutation No [13]
PDB Sequence
YNVFPRTLKW
113
SKMNLTYRIV
123
NYTPDMTHSE
133
VEKAFKKAFK
143
VWSDVTPLNF
153

TRLHDGIADI
163
MISFGIKEHG
173
DFYPFDGPSG
183
LLAHAFPPGP
193
NYGGDAHFDD
203

DETWTSSSKG
213
YNLFLVAAHE
223
FGHSLGLDHS
233
KDPGALMFPI
243
YTYTGKFMLP
255

DDDVQGIQSL
265
YGPGDED
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .5EL or .5EL2 or .5EL3 or :35EL;style chemicals stick;color identity;select .A:183 or .A:184 or .A:185 or .A:186 or .A:218 or .A:219 or .A:222 or .A:223 or .A:232 or .A:236 or .A:237 or .A:238 or .A:239 or .A:241 or .A:242 or .A:243 or .A:244 or .A:245 or .A:246 or .A:247 or .A:252 or .A:255; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
GLY183
3.516
LEU184
3.700
LEU185
2.948
ALA186
4.080
LEU218
3.691
VAL219
3.729
HIS222
3.214
GLU223
3.398
HIS232
4.301
PRO236
4.326
GLY237
3.460
Residue
Distance (Å)
ALA238
4.261
LEU239
3.236
PHE241
3.200
PRO242
2.971
ILE243
3.197
TYR244
3.500
THR245
3.466
TYR246
4.765
THR247
2.423
PHE252
3.733
PRO255
4.013
Ligand Name: Pyrimidine-4,6-dicarboxylic acid bis-(3-methyl-benzylamide) Ligand Info
Structure Description Matrix metalloproteinase-13 complexed with non-zinc binding inhibitor PDB:1XUC
Method X-ray diffraction Resolution 1.70 Å Mutation No [14]
PDB Sequence
YNVFPRTLKW
113
SKMNLTYRIV
123
NYTPDMTHSE
133
VEKAFKKAFK
143
VWSDVTPLNF
153

TRLHDGIADI
163
MISFGIKEHG
173
DFYPFDGPSG
183
LLAHAFPPGP
193
NYGGDAHFDD
203

DETWTSSSKG
213
YNLFLVAAHE
223
FGHSLGLDHS
233
KDPGALMFPI
243
YTYTGKSHFM
253

LPDDDVQGIQ
263
SLYGPGDED
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .PB3 or .PB32 or .PB33 or :3PB3;style chemicals stick;color identity;select .A:140 or .A:185 or .A:215 or .A:217 or .A:218 or .A:219 or .A:222 or .A:237 or .A:238 or .A:239 or .A:240 or .A:241 or .A:242 or .A:243 or .A:244 or .A:245 or .A:246 or .A:247 or .A:248 or .A:249 or .A:250 or .A:251 or .A:252 or .A:255; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
LYS140
3.949
LEU185
4.603
ASN215
4.153
PHE217
3.748
LEU218
3.621
VAL219
3.760
HIS222
3.420
GLY237
3.938
ALA238
3.341
LEU239
3.199
MET240
4.899
PHE241
3.275
Residue
Distance (Å)
PRO242
3.580
ILE243
3.523
TYR244
3.468
THR245
2.664
TYR246
3.599
THR247
2.811
GLY248
4.331
LYS249
3.346
SER250
3.321
HIS251
3.617
PHE252
3.562
PRO255
3.942
Ligand Name: N4,N6-Bis(4-fluoro-3-methylbenzyl)pyrimidine-4,6-dicarboxamide Ligand Info
Structure Description Matrix metalloproteinase-13 complexed with non-zinc binding inhibitor PDB:1XUD
Method X-ray diffraction Resolution 1.80 Å Mutation No [15]
PDB Sequence
YNVFPRTLKW
113
SKMNLTYRIV
123
NYTPDMTHSE
133
VEKAFKKAFK
143
VWSDVTPLNF
153

TRLHDGIADI
163
MISFGIKEHG
173
DFYPFDGPSG
183
LLAHAFPPGP
193
NYGGDAHFDD
203

DETWTSSSKG
213
YNLFLVAAHE
223
FGHSLGLDHS
233
KDPGALMFPI
243
YTYTGKSHFM
253

LPDDDVQGIQ
263
SLYGPGDED
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .PB4 or .PB42 or .PB43 or :3PB4;style chemicals stick;color identity;select .A:140 or .A:185 or .A:215 or .A:217 or .A:218 or .A:219 or .A:222 or .A:223 or .A:237 or .A:238 or .A:239 or .A:240 or .A:241 or .A:242 or .A:243 or .A:244 or .A:245 or .A:246 or .A:247 or .A:248 or .A:249 or .A:250 or .A:251 or .A:252 or .A:255; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
LYS140
3.775
LEU185
3.683
ASN215
3.820
PHE217
3.497
LEU218
3.664
VAL219
3.321
HIS222
3.380
GLU223
4.272
GLY237
4.022
ALA238
3.227
LEU239
3.231
MET240
4.895
PHE241
3.226
Residue
Distance (Å)
PRO242
3.575
ILE243
3.476
TYR244
3.411
THR245
2.641
TYR246
3.611
THR247
2.792
GLY248
4.299
LYS249
3.409
SER250
3.267
HIS251
3.767
PHE252
3.588
PRO255
3.961
Ligand Name: ethyl 5-carbamoyl-1H-indole-2-carboxylate Ligand Info
Structure Description X-RAY Co-structure of MMP-13 with ethyl 5-carbamoyl-1H-indole-2-carboxylate PDB:5BOT
Method X-ray diffraction Resolution 1.85 Å Mutation No [4]
PDB Sequence
YNVFPRTLKW
113
SKMNLTYRIV
123
NYTPDMTHSE
133
VEKAFKKAFK
143
VWSDVTPLNF
153

TRLHDGIADI
163
MISFGIKEHG
173
DFYPFDGPSG
183
LLAHAFPPGP
193
NYGGDAHFDD
203

DETWTSSSKG
213
YNLFLVAAHE
223
FGHSLGLDHS
233
KDPGALMFPI
243
YTYTGFMLPD
256

DDVQGIQSLY
266
GPGDED
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .4UM or .4UM2 or .4UM3 or :34UM;style chemicals stick;color identity;select .A:185 or .A:186 or .A:218 or .A:219 or .A:222 or .A:223 or .A:238 or .A:239 or .A:241 or .A:242 or .A:243 or .A:244 or .A:245 or .A:246 or .A:247 or .A:252; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
LEU185
4.142
ALA186
4.308
LEU218
3.908
VAL219
3.943
HIS222
3.236
GLU223
3.182
ALA238
3.240
LEU239
3.373
Residue
Distance (Å)
PHE241
2.703
PRO242
2.937
ILE243
3.446
TYR244
3.953
THR245
3.029
TYR246
4.168
THR247
2.807
PHE252
2.970
Ligand Name: N,N'-bis(pyridin-3-ylmethyl)pyrimidine-4,6-dicarboxamide Ligand Info
Structure Description Matrix metalloproteinase-13 complexed with non-zinc binding inhibitor PDB:1XUR
Method X-ray diffraction Resolution 1.85 Å Mutation No [15]
PDB Sequence
YNVFPRTLKW
113
SKMNLTYRIV
123
NYTPDMTHSE
133
VEKAFKKAFK
143
VWSDVTPLNF
153

TRLHDGIADI
163
MISFGIKEHG
173
DFYPFDGPSG
183
LLAHAFPPGP
193
NYGGDAHFDD
203

DETWTSSSKG
213
YNLFLVAAHE
223
FGHSLGLDHS
233
KDPGALMFPI
243
YTYTGKSHFM
253

LPDDDVQGIQ
263
SLYGPGDED
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .PB5 or .PB52 or .PB53 or :3PB5;style chemicals stick;color identity;select .A:140 or .A:185 or .A:215 or .A:217 or .A:218 or .A:219 or .A:222 or .A:237 or .A:238 or .A:239 or .A:240 or .A:241 or .A:242 or .A:243 or .A:244 or .A:245 or .A:246 or .A:247 or .A:248 or .A:249 or .A:250 or .A:251 or .A:252 or .A:255; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
LYS140
4.253
LEU185
4.858
ASN215
3.899
PHE217
3.667
LEU218
3.570
VAL219
3.799
HIS222
3.388
GLY237
4.016
ALA238
3.249
LEU239
3.241
MET240
4.887
PHE241
3.262
Residue
Distance (Å)
PRO242
4.025
ILE243
3.567
TYR244
3.389
THR245
2.659
TYR246
3.592
THR247
2.798
GLY248
4.327
LYS249
3.286
SER250
3.519
HIS251
3.835
PHE252
3.569
PRO255
4.054
Ligand Name: (2r)-({[5-(4-Ethoxyphenyl)thiophen-2-Yl]sulfonyl}amino){1-[(1-Methylethoxy)carbonyl]piperidin-4-Yl}ethanoic Acid Ligand Info
Structure Description Crystal Structure of MMP-13 Complexed with Inhibitor 24f PDB:3ELM
Method X-ray diffraction Resolution 1.90 Å Mutation No [16]
PDB Sequence
YNVFPRTLKW
113
SKMNLTYRIV
123
NYTPDMTHSE
133
VEKAFKKAFK
143
VWSDVTPLNF
153

TRLHDGIADI
163
MISFGIKEHG
173
DFYPFDGPSG
183
LLAHAFPPGP
193
NYGGDAHFDD
203

DETWTSSSKG
213
YNLFLVAAHE
223
FGHSLGLDHS
233
KDPGALMFPI
243
YTYFMLPDDD
258

VQGIQSLYGP
268
GDED
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .24F or .24F2 or .24F3 or :324F;style chemicals stick;color identity;select .A:176 or .A:183 or .A:184 or .A:185 or .A:186 or .A:187 or .A:188 or .A:189 or .A:218 or .A:219 or .A:222 or .A:223 or .A:226 or .A:232 or .A:238 or .A:239 or .A:241 or .A:242 or .A:243 or .A:244 or .A:245; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
TYR176
2.835
GLY183
4.491
LEU184
3.580
LEU185
2.798
ALA186
3.214
HIS187
3.586
ALA188
3.269
PHE189
3.975
LEU218
3.660
VAL219
3.827
HIS222
3.412
Residue
Distance (Å)
GLU223
2.667
HIS226
3.448
HIS232
2.931
ALA238
3.889
LEU239
3.505
PHE241
3.247
PRO242
3.389
ILE243
3.494
TYR244
3.586
THR245
3.780
Ligand Name: 5-(4-chlorophenyl)-N-[(1S)-1-cyclohexyl-2-(methylamino)-2-oxoethyl]furan-2-carboxamide Ligand Info
Structure Description MMP-13 in complex with a non zinc-chelating inhibitor PDB:3I7G
Method X-ray diffraction Resolution 1.95 Å Mutation No [17]
PDB Sequence
YNVFPRTLKW
113
SKMNLTYRIV
123
NYTPDMTHSE
133
VEKAFKKAFK
143
VWSDVTPLNF
153

TRLHDGIADI
163
MISFGIKEHG
173
DFYPFDGPSG
183
LLAHAFPPGP
193
NYGGDAHFDD
203

DETWTSSSKG
213
YNLFLVAAHE
223
FGHSLGLDHS
233
KDPGALMFPI
243
YTYTFMLPDD
257

DVQGIQSLYG
267
PGDED
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .732 or .7322 or .7323 or :3732;style chemicals stick;color identity;select .A:183 or .A:184 or .A:185 or .A:186 or .A:214 or .A:218 or .A:219 or .A:222 or .A:223 or .A:238 or .A:239 or .A:241 or .A:242 or .A:243 or .A:244 or .A:245; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
GLY183
3.137
LEU184
3.953
LEU185
3.079
ALA186
3.657
TYR214
3.168
LEU218
3.968
VAL219
3.722
HIS222
3.308
Residue
Distance (Å)
GLU223
2.784
ALA238
4.400
LEU239
3.553
PHE241
2.868
PRO242
3.700
ILE243
3.176
TYR244
3.248
THR245
4.179
Ligand Name: 4-[2-({6-Fluoro-2-[(3-Methoxybenzyl)carbamoyl]-4-Oxo-3,4-Dihydroquinazolin-5-Yl}oxy)ethyl]benzoic Acid Ligand Info
Structure Description Crystal structure of the catalytic domain of MMP-13 complexed with 4-(2-((6-fluoro-2-((3-methoxybenzyl)carbamoyl)-4-oxo-3,4-dihydroquinazolin-5-yl)oxy)ethyl)benzoic acid PDB:3WV1
Method X-ray diffraction Resolution 1.98 Å Mutation No [18]
PDB Sequence
YNVFPRTLKW
113
SKMNLTYRIV
123
NYTPDMTHSE
133
VEKAFKKAFK
143
VWSDVTPLNF
153

TRLHDGIADI
163
MISFGIKEHG
173
DFYPFDGPSG
183
LLAHAFPPGP
193
NYGGDAHFDD
203

DETWTSSSKG
213
YNLFLVAAHE
223
FGHSLGLDHS
233
KDPGALMFPI
243
YTYTGKSHFM
253

LPDDDVQGIQ
263
SLYGPGDEDP
273
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .WHH or .WHH2 or .WHH3 or :3WHH;style chemicals stick;color identity;select .A:140 or .A:185 or .A:209 or .A:215 or .A:217 or .A:218 or .A:219 or .A:222 or .A:223 or .A:237 or .A:238 or .A:239 or .A:240 or .A:241 or .A:242 or .A:243 or .A:244 or .A:245 or .A:246 or .A:247 or .A:249 or .A:250 or .A:251 or .A:252 or .A:253 or .A:255; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
LYS140
2.596
LEU185
3.750
SER209
4.283
ASN215
3.352
PHE217
3.602
LEU218
3.620
VAL219
3.714
HIS222
3.257
GLU223
3.786
GLY237
3.995
ALA238
3.193
LEU239
3.126
MET240
4.821
Residue
Distance (Å)
PHE241
3.066
PRO242
4.009
ILE243
3.372
TYR244
3.598
THR245
2.804
TYR246
3.561
THR247
2.712
LYS249
3.367
SER250
3.805
HIS251
4.084
PHE252
3.694
MET253
3.280
PRO255
3.656
Ligand Name: 4-(1,2,3-Thiadiazol-4-yl)pyridine Ligand Info
Structure Description X-ray structure of MMP-13 in Complex with 4-(1,2,3-thiadiazol-4-yl)pyridine PDB:7JU8
Method X-ray diffraction Resolution 2.00 Å Mutation No [19]
PDB Sequence
YNVFPRTLKW
113
SKMNLTYRIV
123
NYTPDMTHSE
133
VEKAFKKAFK
143
VWSDVTPLNF
153

TRLHDGIADI
163
MISFGIKEHG
173
DFYPFDGPSG
183
LLAHAFPPGP
193
NYGGDAHFDD
203

DETWTSSSKG
213
YNLFLVAAHE
223
FGHSLGLDHS
233
KDPGALMFPI
243
YTYTGKFMLP
255

DDDVQGIQSL
265
YGPGDED
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .9DY or .9DY2 or .9DY3 or :39DY;style chemicals stick;color identity;select .A:185 or .A:218 or .A:219 or .A:222 or .A:223 or .A:238 or .A:239 or .A:240 or .A:241 or .A:242 or .A:243 or .A:244 or .A:245; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
LEU185
3.991
LEU218
4.277
VAL219
3.723
HIS222
3.477
GLU223
3.785
ALA238
3.834
LEU239
3.245
Residue
Distance (Å)
MET240
4.928
PHE241
2.937
PRO242
3.070
ILE243
3.377
TYR244
3.601
THR245
4.022
Ligand Name: Ethyl 5-(1-Methyl-1h-Imidazol-5-Yl)-1h-Indole-2-Carboxylate Ligand Info
Structure Description X-RAY Co-structure of MMP-13 with ethyl 5-(1-methyl-1H-imidazol-5-yl)-1H-indole-2-Carboxylate PDB:5BOY
Method X-ray diffraction Resolution 2.03 Å Mutation No [4]
PDB Sequence
YNVFPRTLKW
113
SKMNLTYRIV
123
NYTPDMTHSE
133
VEKAFKKAFK
143
VWSDVTPLNF
153

TRLHDGIADI
163
MISFGIKEHG
173
DFYPFDGPSG
183
LLAHAFPPGP
193
NYGGDAHFDD
203

DETWTSSSKG
213
YNLFLVAAHE
223
FGHSLGLDHS
233
KDPGALMFPI
243
YTYTGFMLPD
256

DDVQGIQSLY
266
GPGDED
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .4UE or .4UE2 or .4UE3 or :34UE;style chemicals stick;color identity;select .A:185 or .A:218 or .A:219 or .A:222 or .A:223 or .A:237 or .A:238 or .A:239 or .A:240 or .A:241 or .A:242 or .A:243 or .A:244 or .A:245 or .A:246 or .A:247 or .A:252 or .A:255; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
LEU185
4.290
LEU218
3.991
VAL219
3.761
HIS222
3.394
GLU223
4.464
GLY237
3.861
ALA238
3.303
LEU239
3.249
MET240
4.971
Residue
Distance (Å)
PHE241
2.999
PRO242
3.646
ILE243
3.175
TYR244
3.771
THR245
3.155
TYR246
4.505
THR247
2.751
PHE252
3.536
PRO255
3.605
Ligand Name: N-[4-(5-{[(1S)-1-cyclohexyl-2-(methylamino)-2-oxoethyl]carbamoyl}furan-2-yl)phenyl]-1-benzofuran-2-carboxamide Ligand Info
Structure Description MMP-13 in complex with a non zinc-chelating inhibitor PDB:3I7I
Method X-ray diffraction Resolution 2.21 Å Mutation No [17]
PDB Sequence
YNVFPRTLKW
113
SKMNLTYRIV
123
NYTPDMTHSE
133
VEKAFKKAFK
143
VWSDVTPLNF
153

TRLHDGIADI
163
MISFGIKEHG
173
DFYPFDGPSG
183
LLAHAFPPGP
193
NYGGDAHFDD
203

DETWTSSSKG
213
YNLFLVAAHE
223
FGHSLGLDHS
233
KDPGALMFPI
243
YTYTFMLPDD
257

DVQGIQSLYG
267
PGDED
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .518 or .5182 or .5183 or :3518;style chemicals stick;color identity;select .A:182 or .A:183 or .A:184 or .A:185 or .A:186 or .A:214 or .A:218 or .A:219 or .A:222 or .A:223 or .A:237 or .A:238 or .A:239 or .A:241 or .A:242 or .A:243 or .A:244 or .A:245 or .A:246 or .A:247 or .A:252 or .A:253 or .A:255; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
SER182
4.705
GLY183
2.359
LEU184
3.745
LEU185
2.953
ALA186
3.632
TYR214
3.020
LEU218
3.480
VAL219
3.801
HIS222
3.177
GLU223
2.802
GLY237
3.422
ALA238
4.094
Residue
Distance (Å)
LEU239
3.417
PHE241
2.945
PRO242
3.139
ILE243
3.053
TYR244
3.543
THR245
2.485
TYR246
4.568
THR247
2.965
PHE252
3.430
MET253
4.188
PRO255
3.241
Ligand Name: N-(3-Methoxybenzyl)-4-Oxo-3,4-Dihydroquinazoline-2-Carboxamide Ligand Info
Structure Description Crystal structure of the catalytic domain of MMP-13 complexed with N-(3-methoxybenzyl)-4-oxo-3,4-dihydroquinazoline-2-carboxamide PDB:3WV2
Method X-ray diffraction Resolution 2.30 Å Mutation No [11]
PDB Sequence
YNVFPRTLKW
113
SKMNLTYRIV
123
NYTPDMTHSE
133
VEKAFKKAFK
143
VWSDVTPLNF
153

TRLHDGIADI
163
MISFGIKEHG
173
DFYPFDGPSG
183
LLAHAFPPGP
193
NYGGDAHFDD
203

DETWTSSSKG
213
YNLFLVAAHE
223
FGHSLGLDHS
233
KDPGALMFPI
243
YTYTHFMLPD
256

DDVQGIQSLY
266
GPGDED
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .WGG or .WGG2 or .WGG3 or :3WGG;style chemicals stick;color identity;select .A:185 or .A:186 or .A:218 or .A:219 or .A:222 or .A:223 or .A:237 or .A:238 or .A:239 or .A:240 or .A:241 or .A:242 or .A:243 or .A:244 or .A:245 or .A:246 or .A:247 or .A:252 or .A:253 or .A:255; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
LEU185
4.265
ALA186
4.824
LEU218
3.560
VAL219
3.622
HIS222
3.309
GLU223
3.510
GLY237
3.861
ALA238
3.332
LEU239
3.090
MET240
4.797
Residue
Distance (Å)
PHE241
3.001
PRO242
3.673
ILE243
3.338
TYR244
3.543
THR245
2.881
TYR246
3.601
THR247
2.845
PHE252
3.384
MET253
3.458
PRO255
3.546
Ligand Name: Benzyl 6-Benzyl-5,7-Dioxo-6,7-Dihydro-5h-[1,3]thiazolo[3,2-C]pyrimidine-2-Carboxylate Ligand Info
Structure Description Crystal structure analysis of the MMP13 catalytic domain in complex with specific inhibitor PDB:2OW9
Method X-ray diffraction Resolution 1.74 Å Mutation No [1]
PDB Sequence
YNVFPRTLKW
92
SKMNLTYRIV
102
NYTPDMTHSE
112
VEKAFKKAFK
122
VWSDVTPLNF
132

TRLHDGIADI
142
MISFGIKEHG
152
DFYPFDGPSG
162
LLAHAFPPGP
172
NYGGDAHFDD
182

DETWTSSSKG
192
YNLFLVAAHE
202
FGHSLGLDHS
212
KDPGALMFPI
222
YTYTGKSHFM
232

LPDDDVQGIQ
242
SLYGPGD
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .SP6 or .SP62 or .SP63 or :3SP6;style chemicals stick;color identity;select .A:119 or .A:164 or .A:194 or .A:196 or .A:197 or .A:198 or .A:201 or .A:216 or .A:217 or .A:218 or .A:219 or .A:220 or .A:221 or .A:222 or .A:223 or .A:224 or .A:225 or .A:226 or .A:227 or .A:228 or .A:229 or .A:230 or .A:231 or .A:232 or .A:234; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
LYS119
4.817
LEU164
4.646
ASN194
4.852
PHE196
4.098
LEU197
3.649
VAL198
3.800
HIS201
3.411
GLY216
4.497
ALA217
3.234
LEU218
3.133
MET219
4.861
PHE220
3.108
PRO221
3.832
Residue
Distance (Å)
ILE222
3.516
TYR223
3.522
THR224
2.842
TYR225
3.385
THR226
3.039
GLY227
4.847
LYS228
3.336
SER229
3.602
HIS230
3.514
PHE231
3.450
MET232
2.953
PRO234
4.608
Ligand Name: 4-{[1-Methyl-2,4-Dioxo-6-(3-Phenylprop-1-Yn-1-Yl)-1,4-Dihydroquinazolin-3(2h)-Yl]methyl}benzoic Acid Ligand Info
Structure Description MMP13 Catalytic Domain Complexed with 4-{[1-methyl-2,4-dioxo-6-(3-phenylprop-1-yn-1-yl)-1,4-dihydroquinazolin-3(2H)-yl]methyl}benzoic acid PDB:2OZR
Method X-ray diffraction Resolution 2.30 Å Mutation No [1]
PDB Sequence
YNVFPRTLKW
92
SKMNLTYRIV
102
NYTPDMTHSE
112
VEKAFKKAFK
122
VWSDVTPLNF
132

TRLHDGIADI
142
MISFGIKEHG
152
DFYPFDGPSG
162
LLAHAFPPGP
172
NYGGDAHFDD
182

DETWTSSSKG
192
YNLFLVAAHE
202
FGHSLGLDHS
212
KDPGALMFPI
222
YTYTGKSHFM
232

LPDDDVQGIQ
242
SLYGPGD
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .GG1 or .GG12 or .GG13 or :3GG1;style chemicals stick;color identity;select .A:119 or .A:188 or .A:194 or .A:196 or .A:197 or .A:198 or .A:201 or .A:216 or .A:217 or .A:218 or .A:220 or .A:221 or .A:222 or .A:223 or .A:224 or .A:225 or .A:226 or .A:227 or .A:228 or .A:229 or .A:230 or .A:231 or .A:232 or .A:233 or .A:234; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
LYS119
3.278
SER188
4.938
ASN194
3.469
PHE196
3.709
LEU197
3.425
VAL198
4.128
HIS201
3.413
GLY216
4.309
ALA217
3.812
LEU218
3.580
PHE220
2.933
PRO221
3.756
ILE222
3.337
Residue
Distance (Å)
TYR223
3.623
THR224
3.400
TYR225
3.453
THR226
3.096
GLY227
3.354
LYS228
3.412
SER229
3.337
HIS230
4.115
PHE231
3.291
MET232
3.142
LEU233
4.831
PRO234
3.916
Ligand Name: N-[(3s)-1,1-Dioxidotetrahydro-2h-Thiopyran-3-Yl]-4-(4-{[(3s)-3-Hydroxy-1-Azabicyclo[2.2.2]oct-3-Yl]ethynyl}phenoxy)benzamide Ligand Info
Structure Description MMP13 IN COMPLEX WITH A NOVEL SELECTIVE NON ZINC BINDING INHIBITOR CMPD22 PDB:4A7B
Method X-ray diffraction Resolution 2.20 Å Mutation No [20]
PDB Sequence
YNVFPRTLKW
113
SKMNLTYRIV
123
NYTPDMTHSE
133
VEKAFKKAFK
143
VWSDVTPLNF
153

TRLHDGIADI
163
MISFGIKEHG
173
DFYPFDGPSG
183
LLAHAFPPGP
193
NYGGDAHFDD
203

DETWTSSSKG
213
YNLFLVAAHE
223
FGHSLGLDHS
233
KDPGALMFPI
243
YTYTGKSHFM
253

LPDDDVQGIQ
263
SLYGPGDED
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .3W5 or .3W52 or .3W53 or :33W5;style chemicals stick;color identity;select .A:183 or .A:184 or .A:185 or .A:186 or .A:218 or .A:219 or .A:222 or .A:223 or .A:236 or .A:237 or .A:238 or .A:239 or .A:241 or .A:242 or .A:243 or .A:244 or .A:245 or .A:246 or .A:247 or .A:252 or .A:255; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
GLY183
2.682
LEU184
3.451
LEU185
3.038
ALA186
3.675
LEU218
3.685
VAL219
3.669
HIS222
3.233
GLU223
3.383
PRO236
4.322
GLY237
3.396
ALA238
4.236
Residue
Distance (Å)
LEU239
3.138
PHE241
3.349
PRO242
2.912
ILE243
3.243
TYR244
3.386
THR245
3.528
TYR246
4.786
THR247
2.730
PHE252
3.908
PRO255
4.006
Ligand Name: N~2~-[3-(1,1':4',1''-Terphenyl-4-Yl)propanoyl]-L-Alpha-Glutamine Ligand Info
Structure Description Human MMP13 in complex with L-glutamate motif inhibitor PDB:3TVC
Method X-ray diffraction Resolution 2.43 Å Mutation No [21]
PDB Sequence
YNVFPRTLKW
113
SKMNLTYRIV
123
NYTPDMTHSE
133
VEKAFKKAFK
143
VWSDVTPLNF
153

TRLHDGIADI
163
MISFGIKEHG
173
DFYPFDGPSG
183
LLAHAFPPGP
193
NYGGDAHFDD
203

DETWTSSSKG
213
YNLFLVAAHE
223
FGHSLGLDHS
233
KDPGALMFPI
243
YTYTGKSHFM
253

LPDDDVQGIQ
263
SLYGPGDED
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .E3P or .E3P2 or .E3P3 or :3E3P;style chemicals stick;color identity;select .A:183 or .A:184 or .A:185 or .A:186 or .A:187 or .A:218 or .A:219 or .A:222 or .A:223 or .A:226 or .A:232 or .A:237 or .A:238 or .A:239 or .A:241 or .A:242 or .A:243 or .A:244 or .A:245 or .A:246 or .A:247 or .A:252 or .A:255; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
GLY183
4.536
LEU184
3.286
LEU185
2.753
ALA186
3.405
HIS187
4.288
LEU218
3.583
VAL219
3.834
HIS222
3.384
GLU223
2.707
HIS226
3.415
HIS232
3.063
GLY237
4.068
Residue
Distance (Å)
ALA238
3.780
LEU239
3.272
PHE241
3.375
PRO242
3.626
ILE243
3.477
TYR244
3.593
THR245
3.085
TYR246
4.572
THR247
3.599
PHE252
3.788
PRO255
3.966
Ligand Name: 2-{4-[4-(4-Chloro-phenoxy)-benzenesulfonyl]-tetrahydro-pyran-4-YL}-N-hydroxy-acetamide Ligand Info
Structure Description CRYSTAL STRUCTURE OF COLLAGENASE-3 (MMP-13) COMPLEXED TO A DIPHENYL-ETHER SULPHONE BASED HYDROXAMIC ACID PDB:456C
Method X-ray diffraction Resolution 2.40 Å Mutation No [5]
PDB Sequence
TLKWSKMNLT
119
YRIVNYTPDM
129
THSEVEKAFK
139
KAFKVWSDVT
149
PLNFTRLHDG
159

IADIMISFGI
169
KEHGDFYPFD
179
GPSGLLAHAF
189
PPGPNYGGDA
199
HFDDDETWTS
209

SSKGYNLFLV
219
AAHEFGHSLG
229
LDHSKDPGAL
239
MFPIYTYTGK
249
SHFMLPDDDV
259

QGIQSLYGPG
269
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .CBP or .CBP2 or .CBP3 or :3CBP;style chemicals stick;color identity;select .A:183 or .A:184 or .A:185 or .A:186 or .A:187 or .A:188 or .A:218 or .A:219 or .A:222 or .A:223 or .A:226 or .A:232 or .A:238 or .A:239 or .A:240 or .A:241 or .A:242 or .A:243 or .A:244 or .A:245 or .A:246; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
GLY183
3.744
LEU184
3.007
LEU185
1.901
ALA186
1.920
HIS187
3.185
ALA188
3.103
LEU218
3.092
VAL219
2.883
HIS222
2.511
GLU223
2.357
HIS226
2.666
Residue
Distance (Å)
HIS232
2.745
ALA238
3.819
LEU239
2.983
MET240
4.512
PHE241
2.560
PRO242
2.402
ILE243
2.765
TYR244
3.090
THR245
2.637
TYR246
4.866
Ligand Name: trans-4-[(3-{2-[(4-fluorobenzyl)carbamoyl]-6-methylpyridin-4-yl}-1H-1,2,4-triazol-1-yl)methyl]cyclohexanecarboxylic acid Ligand Info
Structure Description Crystal Structure of Human MMP-13 complexed with a (pyridin-4-yl)-2H-tetrazole compound PDB:3KEK
Method X-ray diffraction Resolution 1.97 Å Mutation No [22]
PDB Sequence
YNVFPRTLKW
113
SKMNLTYRIV
123
NYTPDMTHSE
133
VEKAFKKAFK
143
VWSDVTPLNF
153

TRLHDGIADI
163
MISFGIKEHG
173
DFYPFDGPSG
183
LLAHAFPPGP
193
NYGGDAHFDD
203

DETWTSSSKG
213
YNLFLVAAHE
223
FGHSLGLDHS
233
KDPGALMFPI
243
YTYTGKSHFM
253

LPDDDVQGIQ
263
SLYG
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .3EK or .3EK2 or .3EK3 or :33EK;style chemicals stick;color identity;select .A:140 or .A:185 or .A:209 or .A:210 or .A:215 or .A:217 or .A:218 or .A:219 or .A:222 or .A:223 or .A:237 or .A:238 or .A:239 or .A:241 or .A:242 or .A:243 or .A:244 or .A:245 or .A:246 or .A:247 or .A:249 or .A:250 or .A:251 or .A:252 or .A:253 or .A:255; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
LYS140
2.840
LEU185
4.046
SER209
4.160
SER210
4.987
ASN215
3.221
PHE217
3.523
LEU218
3.431
VAL219
3.419
HIS222
3.454
GLU223
4.717
GLY237
3.906
ALA238
3.220
LEU239
3.251
Residue
Distance (Å)
PHE241
3.032
PRO242
3.748
ILE243
3.430
TYR244
3.237
THR245
2.752
TYR246
3.540
THR247
2.931
LYS249
3.384
SER250
3.572
HIS251
3.988
PHE252
3.788
MET253
3.988
PRO255
3.510
Ligand Name: 4-{[({3-[2-(4-Methoxybenzyl)-2h-Tetrazol-5-Yl]phenyl}carbonyl)amino]methyl}benzoic Acid Ligand Info
Structure Description Crystal Structure of Human MMP-13 complexed with a phenyl-2H-tetrazole compound PDB:3KEC
Method X-ray diffraction Resolution 2.05 Å Mutation No [22]
PDB Sequence
YNVFPRTLKW
113
SKMNLTYRIV
123
NYTPDMTHSE
133
VEKAFKKAFK
143
VWSDVTPLNF
153

TRLHDGIADI
163
MISFGIKEHG
173
DFYPFDGPSG
183
LLAHAFPPGP
193
NYGGDAHFDD
203

DETWTSSSKG
213
YNLFLVAAHE
223
FGHSLGLDHS
233
KDPGALMFPI
243
YTYTGKSHFM
253

LPDDDVQGIQ
263
SLYGPGD
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .3KE or .3KE2 or .3KE3 or :33KE;style chemicals stick;color identity;select .A:140 or .A:185 or .A:209 or .A:215 or .A:217 or .A:218 or .A:219 or .A:222 or .A:223 or .A:237 or .A:238 or .A:239 or .A:241 or .A:242 or .A:243 or .A:244 or .A:245 or .A:246 or .A:247 or .A:248 or .A:249 or .A:250 or .A:251 or .A:252 or .A:253 or .A:255; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
LYS140
3.335
LEU185
4.237
SER209
4.711
ASN215
3.017
PHE217
3.515
LEU218
3.642
VAL219
3.469
HIS222
3.413
GLU223
3.515
GLY237
4.232
ALA238
3.687
LEU239
3.418
PHE241
3.003
Residue
Distance (Å)
PRO242
3.676
ILE243
3.322
TYR244
3.461
THR245
2.865
TYR246
3.786
THR247
3.054
GLY248
4.162
LYS249
3.338
SER250
3.627
HIS251
3.621
PHE252
3.395
MET253
4.129
PRO255
4.115
Ligand Name: 4-[(5-{2-[(3-Fluorobenzyl)carbamoyl]pyridin-4-Yl}-2h-Tetrazol-2-Yl)methyl]benzoic Acid Ligand Info
Structure Description Crystal Structure of Human MMP-13 complexed with a (pyridin-4-yl)-2H-tetrazole compound PDB:3KEJ
Method X-ray diffraction Resolution 2.30 Å Mutation No [22]
PDB Sequence
YNVFPRTLKW
113
SKMNLTYRIV
123
NYTPDMTHSE
133
VEKAFKKAFK
143
VWSDVTPLNF
153

TRLHDGIADI
163
MISFGIKEHG
173
DFYPFDGPSG
183
LLAHAFPPGP
193
NYGGDAHFDD
203

DETWTSSSKG
213
YNLFLVAAHE
223
FGHSLGLDHS
233
KDPGALMFPI
243
YTYTGKSHFM
253

LPDDDVQGIQ
263
SLY
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .3EJ or .3EJ2 or .3EJ3 or :33EJ;style chemicals stick;color identity;select .A:140 or .A:185 or .A:209 or .A:215 or .A:217 or .A:218 or .A:219 or .A:222 or .A:223 or .A:237 or .A:238 or .A:239 or .A:240 or .A:241 or .A:242 or .A:243 or .A:244 or .A:245 or .A:246 or .A:247 or .A:248 or .A:249 or .A:250 or .A:251 or .A:252 or .A:253 or .A:255; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
LYS140
2.772
LEU185
4.640
SER209
4.556
ASN215
2.997
PHE217
3.587
LEU218
3.638
VAL219
3.792
HIS222
3.480
GLU223
4.920
GLY237
4.061
ALA238
3.225
LEU239
3.365
MET240
4.992
PHE241
3.168
Residue
Distance (Å)
PRO242
3.377
ILE243
3.344
TYR244
3.473
THR245
2.903
TYR246
3.497
THR247
2.840
GLY248
3.528
LYS249
3.418
SER250
3.593
HIS251
3.713
PHE252
3.590
MET253
4.892
PRO255
4.085
Ligand Name: N-[(2R)-6-amino-1-(hydroxyamino)-1-oxohexan-2-yl]-10-[2-[(diaminomethylideneamino)methyl]phenyl]decanamide Ligand Info
Structure Description Collagenase-3 (MMP-13) complexed to a hydroxamic acid inhibitor PDB:2D1N
Method X-ray diffraction Resolution 2.37 Å Mutation No [23]
PDB Sequence
YNVFPRTLKW
113
SKMNLTYRIV
123
NYTPDMTHSE
133
VEKAFKKAFK
143
VWSDVTPLNF
153

TRLHDGIADI
163
MISFGIKEHG
173
DFYPFDGPSG
183
LLAHAFPPGP
193
NYGGDAHFDD
203

DETWTSSSKG
213
YNLFLVAAHE
223
FGHSLGLDHS
233
KDPGALMFPI
243
YTYTGKSHFM
253

LPDDDVQGIQ
263
SLYGPG
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .FA4 or .FA42 or .FA43 or :3FA4;style chemicals stick;color identity;select .A:176 or .A:183 or .A:184 or .A:185 or .A:186 or .A:187 or .A:218 or .A:219 or .A:222 or .A:223 or .A:226 or .A:232 or .A:236 or .A:237 or .A:238 or .A:239 or .A:240 or .A:241 or .A:242 or .A:243 or .A:244 or .A:245 or .A:247 or .A:252; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
TYR176
3.278
GLY183
3.723
LEU184
3.683
LEU185
2.845
ALA186
3.068
HIS187
4.696
LEU218
3.803
VAL219
4.244
HIS222
2.848
GLU223
2.472
HIS226
3.365
HIS232
2.923
Residue
Distance (Å)
PRO236
2.725
GLY237
4.741
ALA238
2.886
LEU239
3.556
MET240
4.959
PHE241
3.479
PRO242
3.381
ILE243
2.565
TYR244
3.606
THR245
3.011
THR247
3.999
PHE252
3.788
Ligand Name: N-({4'-[(1-Benzofuran-2-ylcarbonyl)amino]-1,1'-biphenyl-4-YL}sulfonyl)-L-valine Ligand Info
Structure Description Crystal structure of the catalytic domain of MMP-13 complexed with WAY-033 PDB:1ZTQ
Method X-ray diffraction Resolution 2.00 Å Mutation No [24]
PDB Sequence
YNVFLKWSKM
91
NLTYRIVNYT
101
PDMTHSEVEK
111
AFKKAFKVWS
121
DVTPLNFTRL
131

HDGIADIMIS
141
FGIKEHGDFY
151
PFDGPSGLLA
161
HAFPPGPNYG
171
GDAHFDDDET
181

WTSSSKGYNL
191
FLVAAHEFGH
201
SLGLDHSKDP
211
GALMFPIYTY
221
TGKSHFMLPD
231

DDVQGIQSLY
241
GP
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .033 or .0332 or .0333 or :3033;style chemicals stick;color identity;select .A:158 or .A:159 or .A:160 or .A:161 or .A:162 or .A:163 or .A:193 or .A:194 or .A:197 or .A:198 or .A:201 or .A:207 or .A:212 or .A:213 or .A:214 or .A:216 or .A:217 or .A:218 or .A:219 or .A:220 or .A:222 or .A:227 or .A:228 or .A:230; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
GLY158
4.781
LEU159
3.345
LEU160
2.858
ALA161
2.858
HIS162
4.048
ALA163
4.905
LEU193
3.665
VAL194
4.188
HIS197
3.471
GLU198
3.086
HIS201
3.424
HIS207
3.072
Residue
Distance (Å)
GLY212
3.325
ALA213
3.581
LEU214
3.132
PHE216
2.925
PRO217
3.120
ILE218
3.099
TYR219
3.288
THR220
3.066
THR222
3.554
PHE227
3.698
MET228
4.849
PRO230
3.498
Ligand Name: Tert-Butyl 4-({[4-(But-2-Yn-1-Ylamino)phenyl]sulfonyl}methyl)-4-[(Hydroxyamino)carbonyl]piperidine-1-Carboxylate Ligand Info
Structure Description Crystal structure of the catalytic domain of MMP-13 complexed with WAY-344 PDB:2PJT
Method X-ray diffraction Resolution 2.80 Å Mutation No [25]
PDB Sequence
YNVFPRTLKW
88
SKMNLTYRIV
98
NYTPDMTHSE
108
VEKAFKKAFK
118
VWSDVTPLNF
128

TRLHDGIADI
138
MISFGIKEHG
148
DFYPFDGPSG
158
LLAHAFPPGP
168
NYGGDAHFDD
178

DETWTSSSKG
188
YNLFLVAAHE
198
FGHSLGLDHS
208
KDPGALMFPI
218
YTYTHFMLPD
231

DDVQGIQSLY
241
GP
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .347 or .3472 or .3473 or :3347;style chemicals stick;color identity;select .A:158 or .A:159 or .A:160 or .A:161 or .A:162 or .A:163 or .A:193 or .A:194 or .A:197 or .A:198 or .A:201 or .A:207 or .A:214 or .A:216 or .A:217 or .A:218 or .A:219 or .A:220; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
GLY158
3.334
LEU159
3.702
LEU160
3.081
ALA161
2.749
HIS162
3.762
ALA163
4.985
LEU193
3.964
VAL194
3.739
HIS197
3.447
Residue
Distance (Å)
GLU198
2.378
HIS201
3.204
HIS207
2.796
LEU214
3.871
PHE216
4.320
PRO217
3.283
ILE218
3.855
TYR219
3.532
THR220
3.286
Ligand Name: 1-(2-Methoxyethyl)-N-Oxo-4-({4-[4-(Trifluoromethoxy)phenoxy]phenyl}sulfonyl)piperidine-4-Carboxamide Ligand Info
Structure Description Crystal structure of MMP-13 in complex with SC-78080 PDB:3KRY
Method X-ray diffraction Resolution 1.90 Å Mutation No [26]
PDB Sequence
YNVFPRTLKW
113
SKMNLTYRIV
123
NYTPDMTHSE
133
VEKAFKKAFK
143
VWSDVTPLNF
153

TRLHDGIADI
163
MISFGIKEHG
173
DFYPFDGPSG
183
LLAHAFPPGP
193
NYGGDAHFDD
203

DETWTSSSKG
213
YNLFLVAAHE
223
FGHSLGLDHS
233
KDPGALMFPI
243
YTYTGKSHFM
253

LPDDDVQGIQ
263
SLYG
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .3KR or .3KR2 or .3KR3 or :33KR;style chemicals stick;color identity;select .A:183 or .A:184 or .A:185 or .A:186 or .A:187 or .A:218 or .A:219 or .A:222 or .A:223 or .A:226 or .A:232 or .A:237 or .A:238 or .A:239 or .A:241 or .A:242 or .A:243 or .A:244 or .A:245 or .A:247 or .A:252; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
GLY183
3.832
LEU184
3.541
LEU185
2.486
ALA186
2.935
HIS187
4.354
LEU218
3.797
VAL219
3.632
HIS222
3.226
GLU223
2.804
HIS226
3.217
HIS232
2.790
Residue
Distance (Å)
GLY237
4.653
ALA238
3.592
LEU239
3.215
PHE241
3.364
PRO242
3.474
ILE243
3.224
TYR244
3.502
THR245
2.866
THR247
3.954
PHE252
4.386
Ligand Name: N-Hydroxy-1-(2-Methoxyethyl)-4-{[4-(3-{5-[4-(Trifluoromethoxy)phenyl]-2h-Tetrazol-2-Yl}propoxy)phenyl]sulfonyl}piperidine-4-Carboxamide Ligand Info
Structure Description MMP-13 in complex with selective tetrazole core inhibitor PDB:3O2X
Method X-ray diffraction Resolution 1.90 Å Mutation No [27]
PDB Sequence
ANVFPRTLKW
1113
SKMNLTYRIV
1123
NYTPDMTHSE
1133
VEKAFKKAFK
1143
VWSDVTPLNF
1153

TRLHDGIADI
1163
MISFGIKEHG
1173
DFYPFDGPSG
1183
LLAHAFPPGP
1193
NYGGDAHFDD
1203

DETWTSSSKG
1213
YNLFLVAAHE
1223
FGHSLGLDHS
1233
KDPGALMFPI
1243
YTYTGKSHFM
1253

LPDDDVQGIQ
1263
SLYG
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .3O2 or .3O22 or .3O23 or :33O2;style chemicals stick;color identity;select .A:1183 or .A:1184 or .A:1185 or .A:1186 or .A:1187 or .A:1188 or .A:1218 or .A:1219 or .A:1222 or .A:1223 or .A:1226 or .A:1232 or .A:1237 or .A:1238 or .A:1239 or .A:1241 or .A:1242 or .A:1243 or .A:1244 or .A:1245 or .A:1246 or .A:1251 or .A:1252 or .A:1253 or .A:1255; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
GLY1183
3.725
LEU1184
3.581
LEU1185
2.837
ALA1186
2.828
HIS1187
4.102
ALA1188
4.941
LEU1218
3.453
VAL1219
4.023
HIS1222
3.076
GLU1223
2.690
HIS1226
3.232
HIS1232
2.896
GLY1237
4.654
Residue
Distance (Å)
ALA1238
3.889
LEU1239
3.233
PHE1241
3.224
PRO1242
3.689
ILE1243
3.279
TYR1244
3.756
THR1245
3.341
TYR1246
3.531
HIS1251
4.133
PHE1252
3.706
MET1253
3.327
PRO1255
3.900
Ligand Name: (2r)-2-[4-(1,3-Benzodioxol-5-Yl)benzyl]-N~4~-Hydroxy-N~1~-[(1s,2r)-2-Hydroxy-2,3-Dihydro-1h-Inden-1-Yl]butanediamide Ligand Info
Structure Description Crystal Structure of Human MMP-13 complexed with an Amino-2-indanol compound PDB:3LJZ
Method X-ray diffraction Resolution 2.00 Å Mutation Yes [28]
PDB Sequence
ANVFPRTLKW
113
SKMNLTYRIV
123
NYTPDMTHSE
133
VEKAFKKAFK
143
VWSDVTPLNF
153

TRLHDGIADI
163
MISFGIKEHG
173
DFYPFDGPSG
183
LLAHAFPPGP
193
NYGGDAHFDD
203

DETWTSSSKG
213
YNLFLVAAHE
223
FGHSLGLDHS
233
KDPGALMFPI
243
YTYTHFMLPD
256

DDVQGIQSLY
266
G
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .LA3 or .LA32 or .LA33 or :3LA3;style chemicals stick;color identity;select .A:183 or .A:184 or .A:185 or .A:186 or .A:187 or .A:188 or .A:218 or .A:219 or .A:222 or .A:223 or .A:226 or .A:232 or .A:238 or .A:239 or .A:241 or .A:242 or .A:243 or .A:244 or .A:245 or .A:247 or .A:252; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
GLY183
3.830
LEU184
3.617
LEU185
2.920
ALA186
2.988
HIS187
3.974
ALA188
4.830
LEU218
3.541
VAL219
4.034
HIS222
3.376
GLU223
2.924
HIS226
3.127
Residue
Distance (Å)
HIS232
2.910
ALA238
3.718
LEU239
3.407
PHE241
3.312
PRO242
3.259
ILE243
3.372
TYR244
2.905
THR245
3.572
THR247
3.898
PHE252
3.839
References  Top
REF 1 Discovery and characterization of a novel inhibitor of matrix metalloprotease-13 that reduces cartilage damage in vivo without joint fibroplasia si... J Biol Chem. 2007 Sep 21;282(38):27781-91.
REF 2 Potent pyrimidinetrione-based inhibitors of MMP-13 with enhanced selectivity over MMP-14. Bioorg Med Chem Lett. 2005 Apr 1;15(7):1807-10.
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