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-(3-chlorobenzyl)-L-prolinamide Ligand Info
Canonical SMILES C1CC(N(C1)C(=O)C(CC2=CC=CC=C2)N)C(=O)NCC3=CC(=CC=C3)Cl
InChI 1S/C21H24ClN3O2/c22-17-9-4-8-16(12-17)14-24-20(26)19-10-5-11-25(19)21(27)18(23)13-15-6-2-1-3-7-15/h1-4,6-9,12,18-19H,5,10-11,13-14,23H2,(H,24,26)/t18-,19+/m1/s1
InChIKey CJHLRGCXPGIPCB-MOPGFXCFSA-N
PubChem Compound ID 25011732
Drug Binding Sites of Target  Top
PDB ID: 2ZC9      Thrombin in complex with Inhibitor
Method X-ray diffraction Resolution 1.58 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
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
3.512
TYR60A
3.519
TRP60D
3.588
GLU97A
3.505
ASN98
3.770
LEU99
3.913
ILE174
3.852
ASP189
3.860
ALA190
3.612
CYS191
3.834
GLU192
4.147
Residue
Distance (Å)
SER195
3.208
VAL213
3.557
SER214
2.830
TRP215
3.198
GLY216
2.890
GLU217
4.325
GLY219
3.648
CYS220
4.176
GLY226
3.739
PHE227
3.436
TYR228
4.147
PDB ID: 5MLS      Thrombin Mutant A190S in complex with (S)-1-(D-phenylalanyl)-N-(3-chlorobenzyl)pyrrolidine-2-carboxamide
Method X-ray diffraction Resolution 1.62 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
WGNLKETGQP
152

SVLQVVNLPI
162
VERPVCKDST
172
RIRITDNMFC
182
AGYKPDEGKR
187
GDSCEGDSGG
197

PFVMKSPFNN
205
RWYQMGIVSW
215
GEGCDRDGKY
225
GFYTHVFRLK
235
KWIQKVIDQF
245
Residue
Distance (Å)
HIS57
3.588
TRP60D
3.440
TYR60A
2.985
GLU97A
3.598
ASN98
3.145
LEU99
3.153
ILE174
3.078
ASP189
4.026
SER190
2.911
CYS191
3.032
GLU192
4.064
Residue
Distance (Å)
SER195
3.230
VAL213
2.947
SER214
2.944
TRP215
2.557
GLY216
2.129
GLU217
3.436
GLY219
3.726
CYS220
4.259
GLY226
3.317
PHE227
3.087
TYR228
4.032
References  Top
REF 1 Think twice: understanding the high potency of bis(phenyl)methane inhibitors of thrombin. J Mol Biol. 2009 Aug 21;391(3):552-64.
REF 2 Thrombin Mutante A190S in complex with (S)-1-((R)-2-amino-3,3-diphenylpropanoyl)-N-(4-carbamimidoylbenzyl)pyrrolidine-2-carboxamide

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