Binding Site Information of Target

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Target General Information
Drug Binding Sites of Target
References
Target General Information  Top
Target ID T54156 Target Info
Target Name Matrix metalloproteinase-9 (MMP-9)
Synonyms Matrix metalloproteinase 9; GELB; CLG4B; 92 kDa type IV collagenase; 92 kDa gelatinase
Target Type Clinical trial Target
Gene Name MMP9
Biochemical Class Peptidase
UniProt ID
MMP9_HUMAN
Drug Binding Sites of Target  Top
Ligand Name: Piperazine Ligand Info
Structure Description Crystal structure of MMP9 in complex with inhibitor BE4. PDB:6ESM
Method X-ray diffraction Resolution 1.10 Å Mutation Yes [1]
PDB Sequence
GDLKWHHHNI
121
TYWIQNYSED
131
LPRAVIDDAF
141
ARAFALWSAV
151
TPLTFTRVYS
161

RDADIVIQFG
171
VAEHGDGYPF
181
DGKDGLLAHA
191
FPPGPGIQGD
201
AHFDDDELWS
211

LGKGVGYSLF
221
LVAAHQFGHA
231
LGLDHSSVPE
241
ALMYPMYRFT
251
EGPPLHKDDV
261

NGIRHLYG
Residue
Distance (Å)
TYR179
3.764
HIS190
3.641
ALA191
3.376
Residue
Distance (Å)
PHE192
3.732
PRO193
4.636
Ligand Name: Cobalt Hexammine Ion Ligand Info
Structure Description Structure determination of a potent, selective antibody inhibitor of human MMP9 (GS-5745 bound to MMP-9) PDB:5TH9
Method X-ray diffraction Resolution 3.00 Å Mutation No [2]
PDB Sequence
TDRQLAEEYL
49
YRYGYTRVAS
66
LGPALLLLQK
76
QLSLPETGEL
86
DSATLKAMRT
96

PRCGVPDLGR
106
FQTFEGDLKW
116
HHHNITYWIQ
126
NYSEDLPRAV
136
IDDAFARAFA
146

LWSAVTPLTF
156
TRVYSRDADI
166
VIQFGVAEHG
176
DGYPFDGKDG
186
LLAHAFPPGP
196

GIQGDAHFDD
206
DELWSLGKGQ
391
GYSLFLVAAH
401
EFGHALGLDH
411
SSVPEALMYP
421

MYRFTEGPPL
431
HKDDVNGIRH
441
LY
Residue
Distance (Å)
SER129
4.003
GLU130
3.389
ASP131
2.970
ASP206
2.922
Residue
Distance (Å)
ASP207
3.901
GLU208
2.875
LEU209
4.454
TRP210
4.978
Ligand Name: ARP100 Ligand Info
Structure Description Crystal structure of an MMP broad spectrum hydroxamate based inhibitor CC27 in complex with the MMP-9 catalytic domain PDB:4H3X
Method X-ray diffraction Resolution 1.76 Å Mutation No [3]
PDB Sequence
GFQTFEGDLK
115
WHHHNITYWI
125
QNYSEDLPRA
135
VIDDAFARAF
145
ALWSAVTPLT
155

FTRVYSRDAD
165
IVIQFGVAEH
175
GDGYPFDGKD
185
GLLAHAFPPG
195
PGIQGDAHFD
205

DDELWSLGKG
215
VGYSLFLVAA
225
HEFGHALGLD
235
HSSVPEALMY
245
PMYRFTEGPP
255

LHKDDVNGIR
265
HLYG
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .10B or .10B2 or .10B3 or :310B;style chemicals stick;color identity;select .A:186 or .A:187 or .A:188 or .A:189 or .A:190 or .A:191 or .A:222 or .A:223 or .A:226 or .A:227 or .A:230 or .A:236 or .A:243 or .A:245 or .A:246 or .A:247 or .A:248 or .A:249; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
GLY186
3.662
LEU187
3.410
LEU188
2.672
ALA189
2.960
HIS190
4.069
ALA191
4.973
LEU222
3.486
VAL223
3.955
HIS226
3.033
Residue
Distance (Å)
GLU227
2.548
HIS230
2.876
HIS236
2.944
LEU243
3.213
TYR245
3.351
PRO246
3.781
MET247
3.445
TYR248
3.783
ARG249
4.949
Ligand Name: 2-Amino-N,3,3-Trimethylbutanamide Ligand Info
Structure Description MMP9 active site mutant-inhibitor complex PDB:1GKD
Method X-ray diffraction Resolution 2.10 Å Mutation Yes [4]
PDB Sequence
FEGDLKWHHH
119
NITYWIQNYS
129
EDLPRAVIDD
139
AFARAFALWS
149
AVTPLTFTRV
159

YSRDADIVIQ
169
FGVAEHGDGY
179
PFDGKDGLLA
189
HAFPPGPGIQ
199
GDAHFDDDEL
209

WSLGKGQGYS
394
LFLVAAHQFG
404
HALGLDHSSV
414
PEALMYPMYR
424
FTEGPPLHKD
434

DVNGIRHLY
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .BUM or .BUM2 or .BUM3 or :3BUM;style chemicals stick;color identity;select .A:186 or .A:187 or .A:188 or .A:393 or .A:421 or .A:422 or .A:423; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
GLY186
3.120
LEU187
4.822
LEU188
3.843
TYR393
3.560
Residue
Distance (Å)
PRO421
3.487
MET422
3.852
TYR423
2.912
Ligand Name: (4s)-3-{[4-(4-Cyano-2-Methylphenyl)piperazin-1-Yl]sulfonyl}-N-Hydroxy-1,3-Thiazolidine-4-Carboxamide Ligand Info
Structure Description Crystal structure MMP-9 complexes with a constrained hydroxamate based inhibitor LT4 PDB:5CUH
Method X-ray diffraction Resolution 1.83 Å Mutation No [5]
PDB Sequence
GFQTFEGDLK
115
WHHHNITYWI
125
QNYSEDLPRA
135
VIDDAFARAF
145
ALWSAVTPLT
155

FTRVYSRDAD
165
IVIQFGVAEH
175
GDGYPFDGKD
185
GLLAHAFPPG
195
PGIQGDAHFD
205

DDELWSLGKG
215
VGYSLFLVAA
225
HEFGHALGLD
235
HSSVPEALMY
245
PMYRFTEGPP
255

LHKDDVNGIR
265
HLYG
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .LTQ or .LTQ2 or .LTQ3 or :3LTQ;style chemicals stick;color identity;select .A:186 or .A:187 or .A:188 or .A:189 or .A:190 or .A:191 or .A:222 or .A:223 or .A:226 or .A:227 or .A:230 or .A:236 or .A:243 or .A:244 or .A:245 or .A:246 or .A:247 or .A:248 or .A:249 or .A:251 or .A:255; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
GLY186
4.182
LEU187
3.640
LEU188
2.714
ALA189
2.887
HIS190
3.945
ALA191
4.726
LEU222
3.254
VAL223
3.834
HIS226
3.133
GLU227
2.652
HIS230
3.158
Residue
Distance (Å)
HIS236
2.868
LEU243
3.364
MET244
4.770
TYR245
3.002
PRO246
3.950
MET247
3.301
TYR248
3.543
ARG249
4.418
THR251
4.505
PRO255
4.724
Ligand Name: 2-{[Formyl(hydroxy)amino]methyl}-4-methylpentanoic acid Ligand Info
Structure Description MMP9 active site mutant-inhibitor complex PDB:1GKD
Method X-ray diffraction Resolution 2.10 Å Mutation Yes [4]
PDB Sequence
FEGDLKWHHH
119
NITYWIQNYS
129
EDLPRAVIDD
139
AFARAFALWS
149
AVTPLTFTRV
159

YSRDADIVIQ
169
FGVAEHGDGY
179
PFDGKDGLLA
189
HAFPPGPGIQ
199
GDAHFDDDEL
209

WSLGKGQGYS
394
LFLVAAHQFG
404
HALGLDHSSV
414
PEALMYPMYR
424
FTEGPPLHKD
434

DVNGIRHLY
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .STN or .STN2 or .STN3 or :3STN;style chemicals stick;color identity;select .A:186 or .A:187 or .A:188 or .A:189 or .A:190 or .A:191 or .A:398 or .A:401 or .A:402 or .A:405 or .A:411 or .A:420 or .A:421 or .A:422 or .A:423; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
GLY186
3.715
LEU187
3.669
LEU188
2.789
ALA189
3.154
HIS190
4.174
ALA191
4.644
VAL398
3.725
HIS401
3.619
Residue
Distance (Å)
GLN402
3.582
HIS405
3.348
HIS411
2.989
TYR420
4.060
PRO421
3.750
MET422
3.751
TYR423
3.626
Ligand Name: N~2~-[(2r)-2-{[formyl(Hydroxy)amino]methyl}-4-Methylpentanoyl]-N,3-Dimethyl-L-Valinamide Ligand Info
Structure Description MMP9-inhibitor complex PDB:1GKC
Method X-ray diffraction Resolution 2.30 Å Mutation No [4]
PDB Sequence
FEGDLKWHHH
119
NITYWIQNYS
129
EDLPRAVIDD
139
AFARAFALWS
149
AVTPLTFTRV
159

YSRDADIVIQ
169
FGVAEHGDGY
179
PFDGKDGLLA
189
HAFPPGPGIQ
199
GDAHFDDDEL
209

WSLGKGQGYS
394
LFLVAAHEFG
404
HALGLDHSSV
414
PEALMYPMYR
424
FTEGPPLHKD
434

DVNGIRHLY
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .NFH or .NFH2 or .NFH3 or :3NFH;style chemicals stick;color identity;select .A:186 or .A:187 or .A:188 or .A:189 or .A:190 or .A:191 or .A:393 or .A:398 or .A:401 or .A:402 or .A:405 or .A:411 or .A:420 or .A:421 or .A:422 or .A:423; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
GLY186
2.898
LEU187
3.514
LEU188
2.786
ALA189
3.363
HIS190
4.156
ALA191
4.561
TYR393
3.513
VAL398
3.820
Residue
Distance (Å)
HIS401
3.556
GLU402
2.733
HIS405
3.005
HIS411
2.899
TYR420
3.873
PRO421
3.425
MET422
3.488
TYR423
2.894
Ligand Name: (2~{S})-2-[2-[4-(4-methoxyphenyl)phenyl]sulfanylphenyl]pentanedioic acid Ligand Info
Structure Description Crystal structure of MMP9 in complex with inhibitor BE4. PDB:6ESM
Method X-ray diffraction Resolution 1.10 Å Mutation Yes [1]
PDB Sequence
GDLKWHHHNI
121
TYWIQNYSED
131
LPRAVIDDAF
141
ARAFALWSAV
151
TPLTFTRVYS
161

RDADIVIQFG
171
VAEHGDGYPF
181
DGKDGLLAHA
191
FPPGPGIQGD
201
AHFDDDELWS
211

LGKGVGYSLF
221
LVAAHQFGHA
231
LGLDHSSVPE
241
ALMYPMYRFT
251
EGPPLHKDDV
261

NGIRHLYG
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set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .B9Z or .B9Z2 or .B9Z3 or :3B9Z;style chemicals stick;color identity;select .A:186 or .A:187 or .A:188 or .A:189 or .A:190 or .A:222 or .A:223 or .A:226 or .A:227 or .A:230 or .A:236 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:251; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
GLY186
3.568
LEU187
3.577
LEU188
3.910
ALA189
3.425
HIS190
3.779
LEU222
4.155
VAL223
3.942
HIS226
3.383
GLN227
2.785
HIS230
3.257
HIS236
3.016
Residue
Distance (Å)
GLU241
4.961
ALA242
3.816
LEU243
3.065
MET244
4.856
TYR245
3.212
PRO246
3.491
MET247
3.231
TYR248
3.585
ARG249
3.424
THR251
3.897
Ligand Name: N-(4-{[(3r)-3-[(Biphenyl-4-Ylsulfonyl)(Propan-2-Yloxy)amino]-4-(Hydroxyamino)-4-Oxobutyl]amino}-4-Oxobutyl)-N'-(4-{[(3s)-3-[(Biphenyl-4-Ylsulfonyl)(Propan-2-Yloxy)amino]-4-(Hydroxyamino)-4-Oxobutyl]amino}-4-Oxobutyl)benzene-1,3-Dicarboxamide Ligand Info
Structure Description Crystal structure of mutant MMP-9 catalytic domain in complex with a twin inhibitor. PDB:4H1Q
Method X-ray diffraction Resolution 1.59 Å Mutation Yes [3]
PDB Sequence
FEGDLKWHHH
119
NITYWIQNYS
129
EDLPRAVIDD
139
AFARAFALWS
149
AVTPLTFTRV
159

YSRDADIVIQ
169
FGVAEHGDGY
179
PFDGKDGLLA
189
HAFPPGPGIQ
199
GDAHFDDDEL
209

WSLGKGQGYS
219
LFLVAAHQFG
229
HALGLDHSSV
239
PEALMYPMYR
249
FTEGPPLHKD
259

DVNGIRHLYG
269
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .0XX or .0XX2 or .0XX3 or :30XX;style chemicals stick;color identity;select .A:178 or .A:179 or .A:180 or .A:181 or .A:182 or .A:186 or .A:187 or .A:188 or .A:189 or .A:190 or .A:191 or .A:192 or .A:193 or .A:222 or .A:223 or .A:226 or .A:227 or .A:230 or .A:234 or .A:236 or .A:242 or .A:243 or .A:245 or .A:246 or .A:247 or .A:248 or .A:249; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
GLY178
4.581
TYR179
3.500
PRO180
3.078
PHE181
3.496
ASP182
3.411
GLY186
3.713
LEU187
3.583
LEU188
2.727
ALA189
3.243
HIS190
3.179
ALA191
2.945
PHE192
3.333
PRO193
3.674
LEU222
3.374
Residue
Distance (Å)
VAL223
3.856
HIS226
2.724
GLN227
2.529
HIS230
2.886
LEU234
4.727
HIS236
3.074
ALA242
4.924
LEU243
3.255
TYR245
3.260
PRO246
3.099
MET247
3.461
TYR248
3.527
ARG249
4.848
Ligand Name: (2r)-4-(1,3-Dioxo-1,3-Dihydro-2h-Isoindol-2-Yl)-N-Hydroxy-2-{[(4'-Methoxybiphenyl-4-Yl)sulfonyl](Propan-2-Yloxy)amino}butanamide Ligand Info
Structure Description Crystal structure of a hydroxamate based inhibitor EN140 in complex with the MMP-9 catalytic domain PDB:4WZV
Method X-ray diffraction Resolution 1.65 Å Mutation No [6]
PDB Sequence
GDLKWHHHNI
121
TYWIQNYSED
131
LPRAVIDDAF
141
ARAFALWSAV
151
TPLTFTRVYS
161

RDADIVIQFG
171
VAEHGDGYPF
181
DGKDGLLAHA
191
FPPGPGIQGD
201
AHFDDDELWS
211

LGKGVGYSLF
221
LVAAHEFGHA
231
LGLDHSSVPE
241
ALMYPMYRFT
251
EGPPLHKDDV
261

NGIRHLYG
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set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .E40 or .E402 or .E403 or :3E40;style chemicals stick;color identity;select .A:186 or .A:187 or .A:188 or .A:189 or .A:190 or .A:191 or .A:222 or .A:223 or .A:226 or .A:227 or .A:230 or .A:234 or .A:235 or .A:236 or .A:242 or .A:243 or .A:245 or .A:246 or .A:247 or .A:248 or .A:249; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
GLY186
3.791
LEU187
3.532
LEU188
2.773
ALA189
2.935
HIS190
3.105
ALA191
2.973
LEU222
3.703
VAL223
4.092
HIS226
3.046
GLU227
2.483
HIS230
2.925
Residue
Distance (Å)
LEU234
4.201
ASP235
3.077
HIS236
2.735
ALA242
4.137
LEU243
3.249
TYR245
3.119
PRO246
3.556
MET247
3.105
TYR248
3.647
ARG249
4.411
Ligand Name: N,N'-Bis(2-{(Biphenyl-4-Ylsulfonyl)[(2r)-1-(Hydroxyamino)-3-Methyl-1-Oxobutan-2-Yl]amino}ethyl)benzene-1,3-Dicarboxamide (Non-Preferred Name) Ligand Info
Structure Description Crystal structure of mutant MMP-9 catalytic domain in complex with a twin inhibitor. PDB:4H82
Method X-ray diffraction Resolution 1.90 Å Mutation Yes [3]
PDB Sequence
FEGDLKWHHH
119
NITYWIQNYS
129
EDLPRAVIDD
139
AFARAFALWS
149
AVTPLTFTRV
159

YSRDADIVIQ
169
FGVAEHGDGY
179
PFDGKDGLLA
189
HAFPPGPGIQ
199
GDAHFDDDEL
209

WSLGKGQGYS
219
LFLVAAHQFG
229
HALGLDHSSV
239
PEALMYPMYR
249
FTEGPPLHKD
259

DVNGIRHLYG
269
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .L29 or .L292 or .L293 or :3L29;style chemicals stick;color identity;select .A:186 or .A:187 or .A:188 or .A:189 or .A:190 or .A:191 or .A:222 or .A:223 or .A:226 or .A:227 or .A:230 or .A:236 or .A:242 or .A:243 or .A:245 or .A:246 or .A:247 or .A:248; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
GLY186
2.608
LEU187
3.584
LEU188
2.822
ALA189
2.749
HIS190
3.284
ALA191
4.765
LEU222
3.383
VAL223
4.144
HIS226
3.106
Residue
Distance (Å)
GLN227
3.360
HIS230
2.715
HIS236
2.768
ALA242
4.664
LEU243
2.892
TYR245
3.093
PRO246
3.379
MET247
3.309
TYR248
3.392
Ligand Name: N,N'-Bis(2-[(Biphenyl-4ylsulfonyl)[(2r)-1-Hydroxy-3-Methyl-1-Oxobutan-2-Yl]-Amino]ethyl)benzene-1,3-Dicarboxamide Ligand Info
Structure Description Crystal structure of an MMP twin carboxylate based inhibitor LC20 in complex with the MMP-9 catalytic domain PDB:4HMA
Method X-ray diffraction Resolution 1.94 Å Mutation Yes [3]
PDB Sequence
FEGDLKWHHH
119
NITYWIQNYS
129
EDLPRAVIDD
139
AFARAFALWS
149
AVTPLTFTRV
159

YSRDADIVIQ
169
FGVAEHGDGY
179
PFDGKDGLLA
189
HAFPPGPGIQ
199
GDAHFDDDEL
209

WSLGKGQGYS
219
LFLVAAHQFG
229
HALGLDHSSV
239
PEALMYPMYR
249
FTEGPPLHKD
259

DVNGIRHLYG
269
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .0ZD or .0ZD2 or .0ZD3 or :30ZD;style chemicals stick;color identity;select .A:186 or .A:187 or .A:188 or .A:189 or .A:190 or .A:191 or .A:222 or .A:223 or .A:226 or .A:227 or .A:230 or .A:236 or .A:243 or .A:245 or .A:246 or .A:247 or .A:248 or .A:249; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
GLY186
4.002
LEU187
3.369
LEU188
2.544
ALA189
3.349
HIS190
3.819
ALA191
4.925
LEU222
3.586
VAL223
3.655
HIS226
3.277
Residue
Distance (Å)
GLN227
3.311
HIS230
3.074
HIS236
2.837
LEU243
3.491
TYR245
3.376
PRO246
3.437
MET247
3.591
TYR248
3.693
ARG249
4.908
Ligand Name: 5-(4-Phenoxyphenyl)-5-(4-Pyrimidin-2-Ylpiperazin-1-Yl)pyrimidine-2,4,6(2h,3h)-Trione Ligand Info
Structure Description MMP-9 active site mutant with barbiturate inhibitor PDB:2OVX
Method X-ray diffraction Resolution 2.00 Å Mutation Yes [7]
PDB Sequence
FEGDLKWHHH
119
NITYWIQNYS
129
EDLPRAVIDD
139
AFARAFALWS
149
AVTPLTFTRV
159

YSRDADIVIQ
169
FGVAEHGDGY
179
PFDGKDGLLA
189
HAFPPGPGIQ
199
GDAHFDDDEL
209

WSLGKGQGYS
394
LFLVAAHQFG
404
HALGLDHSSV
414
PEALMYPMYR
424
FTEGPPLHKD
434

DVNGIRHLY
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .4MR or .4MR2 or .4MR3 or :34MR;style chemicals stick;color identity;select .A:186 or .A:187 or .A:188 or .A:189 or .A:190 or .A:191 or .A:397 or .A:398 or .A:401 or .A:402 or .A:405 or .A:411 or .A:417 or .A:418 or .A:420 or .A:421 or .A:422 or .A:423 or .A:424; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
GLY186
3.719
LEU187
3.700
LEU188
2.882
ALA189
2.670
HIS190
3.893
ALA191
4.606
LEU397
4.145
VAL398
3.889
HIS401
3.305
GLN402
3.146
Residue
Distance (Å)
HIS405
3.465
HIS411
3.216
ALA417
4.010
LEU418
3.167
TYR420
3.475
PRO421
3.143
MET422
3.493
TYR423
3.432
ARG424
3.330
Ligand Name: N-[(4'-Iodobiphenyl-4-Yl)sulfonyl]-D-Tryptophan Ligand Info
Structure Description MMP-9 active site mutant with iodine-labeled carboxylate inhibitor PDB:2OW0
Method X-ray diffraction Resolution 2.00 Å Mutation Yes [7]
PDB Sequence
FEGDLKWHHH
119
NITYWIQNYS
129
EDLPRAVIDD
139
AFARAFALWS
149
AVTPLTFTRV
159

YSRDADIVIQ
169
FGVAEHGDGY
179
PFDGKDGLLA
189
HAFPPGPGIQ
199
GDAHFDDDEL
209

WSLGKGQGYS
394
LFLVAAHQFG
404
HALGLDHSSV
414
PEALMYPMYR
424
FTEGPPLHKD
434

DVNGIRHLY
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .6MR or .6MR2 or .6MR3 or :36MR;style chemicals stick;color identity;select .A:110 or .A:111 or .A:186 or .A:187 or .A:188 or .A:189 or .A:190 or .A:397 or .A:398 or .A:401 or .A:402 or .A:405 or .A:411 or .A:417 or .A:418 or .A:420 or .A:421 or .A:422 or .A:423 or .A:424; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
PHE110
4.049
GLU111
3.003
GLY186
3.835
LEU187
3.802
LEU188
2.852
ALA189
3.031
HIS190
3.948
LEU397
3.799
VAL398
4.095
HIS401
3.377
Residue
Distance (Å)
GLN402
3.033
HIS405
3.294
HIS411
2.963
ALA417
4.791
LEU418
3.452
TYR420
2.958
PRO421
3.334
MET422
3.208
TYR423
3.545
ARG424
4.368
Ligand Name: Nalpha-{(2s)-3-[(S)-Hydroxy(Phenyl)phosphoryl]-2-[(3-Phenylisoxazol-5-Yl)methyl]propanoyl}-L-Tryptophanamide Ligand Info
Structure Description MMP-9 active site mutant with phosphinate inhibitor PDB:2OVZ
Method X-ray diffraction Resolution 2.00 Å Mutation Yes [7]
PDB Sequence
FEGDLKWHHH
119
NITYWIQNYS
129
EDLPRAVIDD
139
AFARAFALWS
149
AVTPLTFTRV
159

YSRDADIVIQ
169
FGVAEHGDGY
179
PFDGKDGLLA
189
HAFPPGPGIQ
199
GDAHFDDDEL
209

WSLGKGQGYS
394
LFLVAAHQFG
404
HALGLDHSSV
414
PEALMYPMYR
424
FTEGPPLHKD
434

DVNGIRHLY
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .5MR or .5MR2 or .5MR3 or :35MR;style chemicals stick;color identity;select .A:110 or .A:182 or .A:186 or .A:187 or .A:188 or .A:189 or .A:190 or .A:191 or .A:393 or .A:397 or .A:398 or .A:401 or .A:402 or .A:405 or .A:411 or .A:417 or .A:418 or .A:420 or .A:421 or .A:422 or .A:423 or .A:424; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
PHE110
3.415
ASP182
3.819
GLY186
3.153
LEU187
3.145
LEU188
2.759
ALA189
3.384
HIS190
3.538
ALA191
4.253
TYR393
4.725
LEU397
4.392
VAL398
3.183
Residue
Distance (Å)
HIS401
3.274
GLN402
2.855
HIS405
3.308
HIS411
2.653
ALA417
4.169
LEU418
3.323
TYR420
2.997
PRO421
3.312
MET422
3.074
TYR423
2.603
ARG424
3.876
Ligand Name: (2r)-2-Amino-3,3,3-Trifluoro-N-Hydroxy-2-{[(4-Phenoxyphenyl)sulfonyl]methyl}propanamide Ligand Info
Structure Description MMP-9 active site mutant with trifluoromethyl hydroxamate inhibitor PDB:2OW1
Method X-ray diffraction Resolution 2.20 Å Mutation Yes [7]
PDB Sequence
FEGDLKWHHH
119
NITYWIQNYS
129
EDLPRAVIDD
139
AFARAFALWS
149
AVTPLTFTRV
159

YSRDADIVIQ
169
FGVAEHGDGY
179
PFDGKDGLLA
189
HAFPPGPGIQ
199
GDAHFDDDEL
209

WSLGKGQGYS
394
LFLVAAHQFG
404
HALGLDHSSV
414
PEALMYPMYR
424
FTEGPPLHKD
434

DVNGIRHLY
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .7MR or .7MR2 or .7MR3 or :37MR;style chemicals stick;color identity;select .A:186 or .A:187 or .A:188 or .A:189 or .A:190 or .A:191 or .A:397 or .A:398 or .A:401 or .A:402 or .A:405 or .A:411 or .A:417 or .A:418 or .A:420 or .A:421 or .A:422 or .A:423 or .A:424; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
GLY186
3.673
LEU187
3.840
LEU188
2.957
ALA189
3.053
HIS190
4.103
ALA191
4.919
LEU397
3.890
VAL398
3.941
HIS401
2.868
GLN402
2.926
Residue
Distance (Å)
HIS405
3.172
HIS411
2.801
ALA417
4.368
LEU418
3.122
TYR420
3.461
PRO421
3.285
MET422
3.698
TYR423
3.313
ARG424
3.336
Ligand Name: (3r)-4,4-Difluoro-3-[(4-Methoxyphenyl)sulfonyl]butanoic Acid Ligand Info
Structure Description MMP-9 active site mutant with difluoro butanoic acid inhibitor PDB:2OW2
Method X-ray diffraction Resolution 2.90 Å Mutation Yes [7]
PDB Sequence
DLKWHHHNIT
122
YWIQNYSEDL
132
PRAVIDDAFA
142
RAFALWSAVT
152
PLTFTRVYSR
162

DADIVIQFGV
172
AEHGDGYPFD
182
GKDGLLAHAF
192
PPGPGIQGDA
202
HFDDDELWSL
212

GKGQGYSLFL
397
VAAHQFGHAL
407
GLDHSSVPEA
417
LMYPMYRFTE
427
GPPLHKDDVN
437

GIRHLY
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .8MR or .8MR2 or .8MR3 or :38MR;style chemicals stick;color identity;select .A:186 or .A:187 or .A:188 or .A:189 or .A:190 or .A:191 or .A:397 or .A:398 or .A:401 or .A:402 or .A:405 or .A:411 or .A:418 or .A:420 or .A:421 or .A:422 or .A:423 or .A:424; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
GLY186
4.180
LEU187
3.530
LEU188
3.321
ALA189
2.655
HIS190
3.592
ALA191
4.745
LEU397
4.487
VAL398
3.661
HIS401
3.076
Residue
Distance (Å)
GLN402
2.746
HIS405
3.656
HIS411
3.249
LEU418
4.475
TYR420
3.698
PRO421
2.936
MET422
4.412
TYR423
3.377
ARG424
4.664
Ligand Name: (2R)-3-methyl-N-oxo-2-[(4-phenylphenyl)sulfonyl-propan-2-yloxyamino]butanamide Ligand Info
Structure Description Crystal structure of a hydroxamate based inhibitor ARP101 (EN73) in complex with the MMP-9 catalytic domain. PDB:4XCT
Method X-ray diffraction Resolution 1.30 Å Mutation No [6]
PDB Sequence
DLKWHHHNIT
122
YWIQNYSEDL
132
PRAVIDDAFA
142
RAFALWSAVT
152
PLTFTRVYSR
162

DADIVIQFGV
172
AEHGDGYPFD
182
GKDGLLAHAF
192
PPGPGIQGDA
202
HFDDDELWSL
212

GKGVGYSLFL
222
VAAHEFGHAL
232
GLDHSSVPEA
242
LMYPMYRFTE
252
GPPLHKDDVN
262

GIRHLYG
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .N73 or .N732 or .N733 or :3N73;style chemicals stick;color identity;select .A:186 or .A:187 or .A:188 or .A:189 or .A:190 or .A:191 or .A:222 or .A:223 or .A:226 or .A:227 or .A:230 or .A:236 or .A:243 or .A:245 or .A:246 or .A:247 or .A:248; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
GLY186
3.829
LEU187
3.441
LEU188
2.922
ALA189
2.869
HIS190
3.995
ALA191
4.963
LEU222
3.423
VAL223
3.891
HIS226
3.219
Residue
Distance (Å)
GLU227
2.594
HIS230
3.055
HIS236
2.884
LEU243
3.144
TYR245
3.045
PRO246
3.575
MET247
3.450
TYR248
3.668
Ligand Name: (2S,3S)-butane-2,3-diol Ligand Info
Structure Description Crystal structure of a hydroxamate based inhibitor ARP101 (EN73) in complex with the MMP-9 catalytic domain. PDB:4XCT
Method X-ray diffraction Resolution 1.30 Å Mutation No [6]
PDB Sequence
DLKWHHHNIT
122
YWIQNYSEDL
132
PRAVIDDAFA
142
RAFALWSAVT
152
PLTFTRVYSR
162

DADIVIQFGV
172
AEHGDGYPFD
182
GKDGLLAHAF
192
PPGPGIQGDA
202
HFDDDELWSL
212

GKGVGYSLFL
222
VAAHEFGHAL
232
GLDHSSVPEA
242
LMYPMYRFTE
252
GPPLHKDDVN
262

GIRHLYG
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .BUD or .BUD2 or .BUD3 or :3BUD;style chemicals stick;color identity;select .A:130 or .A:131 or .A:132 or .A:133; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
GLU130
3.134
ASP131
4.104
Residue
Distance (Å)
LEU132
3.314
PRO133
3.485
Ligand Name: (2R)-2-[{(E)-2-[({(2R,3R,4R,5S,6R)-3-(acetylamino)-4,5-bis(acetyloxy)-6-[(acetyloxy)methyl]tetrahydro-2H-pyran-2-yl}carbamothioyl)amino]ethenyl}(biphenyl-4-ylsulfonyl)amino]-3-methylbutanoic acid (non-preferred name) Ligand Info
Structure Description Crystal structure of the catalytic domain of MMP-9 in complex with a selective sugar-conjugated arylsulfonamide carboxylate water-soluble inhibitor (DC27). PDB:5I12
Method X-ray diffraction Resolution 1.59 Å Mutation No [8]
PDB Sequence
DLKWHHHNIT
122
YWIQNYSEDL
132
PRAVIDDAFA
142
RAFALWSAVT
152
PLTFTRVYSR
162

DADIVIQFGV
172
AEHGDGYPFD
182
GKDGLLAHAF
192
PPGPGIQGDA
202
HFDDDELWSL
212

GKGVGYSLFL
222
VAAHEFGHAL
232
GLDHSSVPEA
242
LMYPMYRFTE
252
GPPLHKDDVN
262

GIRHLYG
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .H27 or .H272 or .H273 or :3H27;style chemicals stick;color identity;select .A:186 or .A:187 or .A:188 or .A:189 or .A:190 or .A:191 or .A:222 or .A:223 or .A:226 or .A:227 or .A:230 or .A:236 or .A:243 or .A:245 or .A:246 or .A:247 or .A:248 or .A:249; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
GLY186
4.209
LEU187
3.525
LEU188
3.042
ALA189
3.208
HIS190
3.702
ALA191
4.796
LEU222
3.625
VAL223
3.954
HIS226
3.380
Residue
Distance (Å)
GLU227
2.555
HIS230
3.432
HIS236
2.878
LEU243
3.423
TYR245
3.129
PRO246
3.301
MET247
3.646
TYR248
3.742
ARG249
4.844
References  Top
REF 1 Development of Thioaryl-Based Matrix Metalloproteinase-12 Inhibitors with Alternative Zinc-Binding Groups: Synthesis, Potentiometric, NMR, and Crystallographic Studies. J Med Chem. 2018 May 24;61(10):4421-4435.
REF 2 Biochemical characterization and structure determination of a potent, selective antibody inhibitor of human MMP9. J Biol Chem. 2017 Apr 21;292(16):6810-6820.
REF 3 Crystallization of bi-functional ligand protein complexes. J Struct Biol. 2013 Jun;182(3):246-54.
REF 4 Crystal structure of human MMP9 in complex with a reverse hydroxamate inhibitor. J Mol Biol. 2002 May 24;319(1):173-81.
REF 5 Discovery of a new selective inhibitor of A Disintegrin And Metalloprotease 10 (ADAM-10) able to reduce the shedding of NKG2D ligands in Hodgkin's lymphoma cell models. Eur J Med Chem. 2016 Mar 23;111:193-201.
REF 6 N-O-Isopropyl Sulfonamido-Based Hydroxamates as Matrix Metalloproteinase Inhibitors: Hit Selection and in Vivo Antiangiogenic Activity. J Med Chem. 2015 Sep 24;58(18):7224-40.
REF 7 Crystal structures of MMP-9 complexes with five inhibitors: contribution of the flexible Arg424 side-chain to selectivity. J Mol Biol. 2007 Aug 24;371(4):989-1006.
REF 8 Sugar-Based Arylsulfonamide Carboxylates as Selective and Water-Soluble Matrix Metalloproteinase-12 Inhibitors. ChemMedChem. 2016 Aug 5;11(15):1626-37.

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