Target Binding Site Detail

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Target General Information
Ligand General Information
Drug Binding Sites of Target
References
Target General Information  Top
Target ID T94033 Target Info
Target Name Coagulation factor IIa (F2)
Synonyms Prothrombin; Coagulation factor II
Target Type Successful Target
Gene Name F2
Biochemical Class Peptidase
UniProt ID
THRB_HUMAN
Ligand General Information  Top
Ligand Name PPACK Ligand Info
Canonical SMILES C1CC(N(C1)C(=O)C(CC2=CC=CC=C2)N)C(=O)NC(CCCN=C(N)N)C(=O)CCl
InChI 1S/C21H31ClN6O3/c22-13-18(29)16(8-4-10-26-21(24)25)27-19(30)17-9-5-11-28(17)20(31)15(23)12-14-6-2-1-3-7-14/h1-3,6-7,15-17H,4-5,8-13,23H2,(H,27,30)(H4,24,25,26)/t15-,16+,17+/m1/s1
InChIKey KWPACVJPAFGBEQ-IKGGRYGDSA-N
PubChem Compound ID 5311176
Drug Binding Sites of Target  Top
PDB ID: 1HUT      THE STRUCTURE OF ALPHA-THROMBIN INHIBITED BY A 15-MER SINGLE-STRANDED DNA APTAMER
Method X-ray diffraction Resolution 2.90 Å Mutation No [1]
PDB Sequence
IVEGSDAEIG
25
MSPWQVMLFR
35
KSPQELLCGA
44
SLISDRWVLT
54
AAHCLLYPPW
60D

DKNFTENDLL
65
VRIGKHSRTR
75
YERNIEKISM
84
LEKIYIHPRY
94
NWRENLDRDI
103

ALMKLKKPVA
113
FSDYIHPVCL
123
PDRETAASLL
130
QAGYKGRVTG
140
WGNLKETWGQ
151

PSVLQVVNLP
161
IVERPVCKDS
171
TRIRITDNMF
181
CAGYKPDEGK
186D
RGDACEGDSG
196

GPFVMKSPFN
204B
NRWYQMGIVS
214
WGEGCDRDGK
224
YGFYTHVFRL
234
KKWIQKVIDQ
244

FGE
Residue
Distance (Å)
HIS57
2.324
CYS58
4.984
TYR60A
2.945
TRP60D
3.541
LYS60F
4.442
TRP96
4.896
GLU97A
4.386
ASN98
3.454
LEU99
3.080
ILE174
3.420
ASP189
2.271
ALA190
2.521
CYS191
3.331
GLU192
4.134
Residue
Distance (Å)
GLY193
4.345
ASP194
4.205
SER195
2.373
VAL213
4.636
SER214
2.407
TRP215
3.007
GLY216
3.049
GLY219
4.178
CYS220
3.427
ASP221
4.360
TYR225
4.644
GLY226
4.170
TYR228
4.789
PDB ID: 3PMH      Mechanism of Sulfotyrosine-Mediated Glycoprotein Ib Interaction with Two Distinct alpha-Thrombin Sites
Method X-ray diffraction Resolution 3.20 Å Mutation Yes [2]
PDB Sequence
IVEGSDAEIG
25
MSPWQVMLFR
35
KSPQELLCGA
44
SLISDRWVLT
54
AAHCLLYPPW
60D

DKNFTENDLL
65
VRIGKHSRTR
75
YERNIEKISM
84
LEKIYIHPRY
94
NWRENLDRDI
103

ALMKLKKPVA
113
FSDYIHPVCL
123
PDRETAASLL
130
QAGYKGRVTG
140
WGNLKETWTA
149A

NVGKGQPSVL
155
QVVNLPIVER
165
PVCKDSTRIR
175
ITDNMFCAGY
184A
KPDEGKRGDA
190

CEGDSGGPFV
200
MKSPFNNRWY
208
QMGIVSWGEG
219
CDRDGKYGFY
228
THVFRLKKWI
238

QKVIDQFGE
Residue
Distance (Å)
LEU41
4.681
CYS42
4.237
HIS57
2.244
CYS58
4.385
TYR60A
3.388
TRP60D
4.047
GLU97A
3.475
ASN98
3.850
LEU99
3.734
ILE174
3.423
ASP189
2.707
ALA190
3.503
CYS191
3.814
GLU192
3.290
Residue
Distance (Å)
GLY193
2.387
ASP194
3.762
SER195
2.221
VAL213
4.119
SER214
3.135
TRP215
2.833
GLY216
2.512
GLU217
3.961
GLY219
2.574
CYS220
3.752
ASP221A
4.740
GLY226
3.873
PHE227
4.983
PDB ID: 2HPP      Structures of the noncovalent complexes of human and bovine prothrombin fragment 2 with human ppack-thrombin
Method X-ray diffraction Resolution 3.30 Å Mutation No [3]
PDB Sequence
IVEGSDAEIG
25
MSPWQVMLFR
35
KSPQELLCGA
44
SLISDRWVLT
54
AAHCLLYPPW
60D

DKNFTENDLL
65
VRIGKHSRTR
75
YERNIEKISM
84
LEKIYIHPRY
94
NWRENLDRDI
103

ALMKLKKPVA
113
FSDYIHPVCL
123
PDRETAASLL
130
QAGYKGRVTG
140
WGNLKETWGQ
151

PSVLQVVNLP
161
IVERPVCKDS
171
TRIRITDNMF
181
CAGYKPDEGK
186D
RGDACEGDSG
196

GPFVMKSPFN
204B
NRWYQMGIVS
214
WGEGCDRDGK
224
YGFYTHVFRL
234
KKWIQKVIDQ
244

F
Residue
Distance (Å)
CYS42
4.697
HIS57
1.711
TYR60A
3.544
TRP60D
3.927
GLU97A
3.517
ASN98
3.922
LEU99
3.529
ILE174
3.190
ASP189
2.965
ALA190
2.676
CYS191
3.677
GLU192
3.939
GLY193
3.581
Residue
Distance (Å)
ASP194
4.038
SER195
2.225
VAL213
3.891
SER214
2.868
TRP215
2.663
GLY216
3.150
GLU217
4.672
GLY219
3.359
CYS220
3.813
ASP221
4.864
GLY226
4.038
PHE227
4.788
PDB ID: 2HPQ      Structures of the noncovalent complexes of human and bovine prothrombin fragment 2 with human ppack-thrombin
Method X-ray diffraction Resolution 3.30 Å Mutation No [3]
PDB Sequence
IVEGSDAEIG
25
MSPWQVMLFR
35
KSPQELLCGA
44
SLISDRWVLT
54
AAHCLLYPPW
60D

DKNFTENDLL
65
VRIGKHSRTR
75
YERNIEKISM
84
LEKIYIHPRY
94
NWRENLDRDI
103

ALMKLKKPVA
113
FSDYIHPVCL
123
PDRETAASLL
130
QAGYKGRVTG
140
WGNLKETWGQ
151

PSVLQVVNLP
161
IVERPVCKDS
171
TRIRITDNMF
181
CAGYKPDEGK
186D
RGDACEGDSG
196

GPFVMKSPFN
204B
NRWYQMGIVS
214
WGEGCDRDGK
224
YGFYTHVFRL
234
KKWIQKVIDQ
244

F
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .0G7 or .0G72 or .0G73 or :30G7;style chemicals stick;color identity;select .H:42 or .H:57 or .H:58 or .H:60A or .H:60D or .H:97A or .H:98 or .H:99 or .H:174 or .H:189 or .H:190 or .H:191 or .H:192 or .H:193 or .H:194 or .H:195 or .H:213 or .H:214 or .H:215 or .H:216 or .H:217 or .H:219 or .H:220 or .H:226; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
CYS42
4.550
HIS57
1.589
CYS58
4.196
TYR60A
3.658
TRP60D
3.614
GLU97A
3.924
ASN98
4.009
LEU99
3.665
ILE174
3.611
ASP189
2.978
ALA190
3.316
CYS191
3.649
Residue
Distance (Å)
GLU192
3.699
GLY193
3.410
ASP194
3.903
SER195
2.119
VAL213
4.205
SER214
3.101
TRP215
2.978
GLY216
2.863
GLU217
4.692
GLY219
3.302
CYS220
4.043
GLY226
4.571
References  Top
REF 1 The structure of alpha-thrombin inhibited by a 15-mer single-stranded DNA aptamer. J Biol Chem. 1993 Aug 25;268(24):17651-4.
REF 2 Binding of alpha-thrombin to surface-anchored platelet glycoprotein Ib(alpha) sulfotyrosines through a two-site mechanism involving exosite I. Proc Natl Acad Sci U S A. 2011 May 24;108(21):8628-33.
REF 3 Structures of the noncovalent complexes of human and bovine prothrombin fragment 2 with human PPACK-thrombin. Biochemistry. 1993 May 11;32(18):4727-37.

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