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 Melagatran Ligand Info
Canonical SMILES C1CCC(CC1)C(C(=O)N2CCC2C(=O)NCC3=CC=C(C=C3)C(=N)N)NCC(=O)O
InChI 1S/C22H31N5O4/c23-20(24)16-8-6-14(7-9-16)12-26-21(30)17-10-11-27(17)22(31)19(25-13-18(28)29)15-4-2-1-3-5-15/h6-9,15,17,19,25H,1-5,10-13H2,(H3,23,24)(H,26,30)(H,28,29)/t17-,19+/m0/s1
InChIKey DKWNMCUOEDMMIN-PKOBYXMFSA-N
PubChem Compound ID 183797
Drug Binding Sites of Target  Top
PDB ID: 1K22      HUMAN THROMBIN-INHIBITOR COMPLEX
Method X-ray diffraction Resolution 1.93 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
3.403
TYR60A
3.475
TRP60D
3.000
GLU97A
3.840
ASN98
4.273
LEU99
3.682
ILE174
3.540
ASP189
2.734
ALA190
3.130
CYS191
3.871
GLU192
3.903
GLY193
4.992
Residue
Distance (Å)
SER195
3.029
VAL213
3.872
SER214
3.338
TRP215
3.061
GLY216
2.952
GLU217
3.278
GLY219
2.826
CYS220
3.691
ASP221
4.599
GLY226
3.273
PHE227
4.346
TYR228
4.931
PDB ID: 4BAH      Thrombin in complex with inhibitor
Method X-ray diffraction Resolution 1.94 Å Mutation No [2]
PDB Sequence
IVEGSDAEIG
46
MSPWQVMLFR
56
KSPQELLCGA
66
SLISDRWVLT
76
AAHCLLYPPW
86

DKNFTENDLL
96
VRIGKHSRTR
106
YERNIEKISM
116
LEKIYIHPRY
126
NWRENLDRDI
136

ALMKLKKPVA
146
FSDYIHPVCL
156
PDRETAASLL
166
QAGYKGRVTG
176
WGNLKETWGQ
186

PSVLQVVNLP
196
IVERPVCKDS
206
TRIRITDNMF
216
CAGYKPDEGK
226
RGDACEGDSG
236

GPFVMKSPFN
246
NRWYQMGIVS
256
WGEGCDRDGK
266
YGFYTHVFRL
276
KKWIQKVIDQ
286

FGE
Residue
Distance (Å)
HIS79
3.331
TYR83
3.419
TRP86
3.083
GLU130
3.794
ASN131
4.239
LEU132
2.845
ASP135
4.918
ILE209
3.608
ASP229
2.691
ALA230
3.073
CYS231
3.858
GLU232
4.074
Residue
Distance (Å)
SER235
3.089
VAL255
3.826
SER256
2.910
TRP257
3.138
GLY258
2.914
GLU259
3.392
GLY260
2.878
CYS261
3.725
ASP262
4.685
GLY268
3.395
PHE269
4.414
TYR270
4.916
References  Top
REF 1 Factorising ligand affinity: a combined thermodynamic and crystallographic study of trypsin and thrombin inhibition. J Mol Biol. 2001 Oct 26;313(3):593-614.
REF 2 Identification of structural-kinetic and structural-thermodynamic relationships for thrombin inhibitors. Biochemistry. 2013 Jan 29;52(4):613-26.

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