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 D-Phenylalanyl-N-{4-[amino(Iminio)methyl]benzyl}-L-Prolinamide Ligand Info
Canonical SMILES C1CC(N(C1)C(=O)C(CC2=CC=CC=C2)N)C(=O)NCC3=CC=C(C=C3)C(=[NH2+])N
InChI 1S/C22H27N5O2/c23-18(13-15-5-2-1-3-6-15)22(29)27-12-4-7-19(27)21(28)26-14-16-8-10-17(11-9-16)20(24)25/h1-3,5-6,8-11,18-19H,4,7,12-14,23H2,(H3,24,25)(H,26,28)/p+1/t18-,19+/m1/s1
InChIKey VZFTWWJAUZOJDH-MOPGFXCFSA-O
PubChem Compound ID 46937043
Drug Binding Sites of Target  Top
PDB ID: 5MM6      Thrombin Mutant A190S in complex with (S)-1-(D-phenylalanyl)-N-(4-carbamimidoylbenzyl)pyrrolidine-2-carboxamide
Method X-ray diffraction Resolution 1.29 Å Mutation Yes [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
WGNLKETGQP
152

SVLQVVNLPI
162
VERPVCKDST
172
RIRITDNMFC
182
AGYKPDEGKR
187
GDSCEGDSGG
197

PFVMKSPFNN
205
RWYQMGIVSW
215
GEGCDRDGKY
225
GFYTHVFRLK
235
KWIQKVIDQF
245

G
Residue
Distance (Å)
HIS57
3.570
TRP60D
3.061
TYR60A
3.374
GLU97A
3.441
ASN98
3.097
LEU99
3.135
ILE174
2.984
ASP189
2.805
SER190
3.065
CYS191
3.302
GLU192
3.595
GLY193
4.949
ASP194
4.756
Residue
Distance (Å)
SER195
3.124
VAL213
3.108
SER214
2.964
TRP215
2.476
GLY216
2.293
GLU217
3.460
GLY219
2.847
CYS220
2.901
ASP221
4.147
GLY226
3.008
PHE227
4.145
TYR228
4.540
PDB ID: 2ZDA      Exploring Thrombin S1 pocket
Method X-ray diffraction Resolution 1.73 Å Mutation No [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
WGNLKETGQP
152

SVLQVVNLPI
162
VERPVCKDST
172
RIRITDNMFC
182
AGYKPDEGKR
187
GDACEGDSGG
197

PFVMKSPFNN
205
RWYQMGIVSW
215
GEGCDRDGKY
225
GFYTHVFRLK
235
KWIQKVIDQF
245

G
Residue
Distance (Å)
HIS57
3.475
TYR60A
3.460
TRP60D
3.818
GLU97A
3.305
ASN98
3.899
LEU99
3.743
ILE174
3.652
ASP189
2.793
ALA190
3.187
CYS191
4.077
GLU192
4.359
SER195
3.091
Residue
Distance (Å)
VAL213
3.678
SER214
2.903
TRP215
3.107
GLY216
2.780
GLU217
4.426
GLY219
2.915
CYS220
3.733
ASP221
4.712
GLY226
3.499
PHE227
4.588
TYR228
4.930
References  Top
REF 1 Thrombin Mutant A190S in complex with (S)-1-(D-phenylalanyl)-N-(4-carbamimidoylbenzyl)pyrrolidine-2-carboxamide
REF 2 Think twice: understanding the high potency of bis(phenyl)methane inhibitors of thrombin. J Mol Biol. 2009 Aug 21;391(3):552-64.

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