Target Binding Site Detail

Content Navigation (  All   None )                                      
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 (2s)-N-[[2-(Aminomethyl)-5-Chloro-Phenyl]methyl]-1-[(2r)-5-Carbamimidamido-2-(Phenylmethylsulfonylamino)pentanoyl]pyrrolidine-2-Carboxamide Ligand Info
Canonical SMILES C1CC(N(C1)C(=O)C(CCCN=C(N)N)NS(=O)(=O)CC2=CC=CC=C2)C(=O)NCC3=C(C=CC(=C3)Cl)CN
InChI 1S/C26H36ClN7O4S/c27-21-11-10-19(15-28)20(14-21)16-32-24(35)23-9-5-13-34(23)25(36)22(8-4-12-31-26(29)30)33-39(37,38)17-18-6-2-1-3-7-18/h1-3,6-7,10-11,14,22-23,33H,4-5,8-9,12-13,15-17,28H2,(H,32,35)(H4,29,30,31)/t22-,23+/m1/s1
InChIKey MWLLGEVAEDIFRC-PKTZIBPZSA-N
PubChem Compound ID 44144381
Drug Binding Sites of Target  Top
PDB ID: 5JFD      Thrombin in complex with (S)-N-(2-(aminomethyl)-5-chlorobenzyl)-1-((benzylsulfonyl)-D-arginyl)pyrrolidine-2-carboxamide
Method X-ray diffraction Resolution 1.46 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

FG
Residue
Distance (Å)
HIS57
3.488
TRP60D
3.036
TYR60A
3.714
LEU99
3.347
THR172
4.096
ARG173
4.378
ILE174
2.700
ASP189
3.587
ALA190
2.864
CYS191
3.205
GLU192
3.681
SER195
2.785
Residue
Distance (Å)
VAL213
2.889
SER214
2.925
TRP215
2.695
GLY216
2.107
GLU217
2.763
GLY219
2.219
CYS220
3.788
ARG221A
3.503
LYS224
4.810
GLY226
3.253
PHE227
3.100
TYR228
3.960
PDB ID: 3EQ0      Thrombin Inhibitor
Method X-ray diffraction Resolution 1.53 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
WGNLKEQPSV
154

LQVVNLPIVE
164
RPVCKDSTRI
174
RITDNMFCAG
184
YKPDEGKRGD
189
ACEGDSGGPF
199

VMKSPFNNRW
207
YQMGIVSWGE
217
GCDRDGKYGF
227
YTHVFRLKKW
237
IQKVID
Residue
Distance (Å)
HIS57
3.402
TRP60D
3.723
TYR60A
3.880
GLU97A
2.942
ASN98
4.815
LEU99
4.211
ILE174
2.681
ASP189
3.659
ALA190
3.484
CYS191
3.775
GLU192
3.781
SER195
3.295
Residue
Distance (Å)
VAL213
3.563
SER214
3.058
TRP215
3.412
GLY216
2.910
GLU217
3.490
GLY219
3.167
CYS220
3.743
ARG221A
3.965
GLY226
3.882
PHE227
3.337
TYR228
3.982
References  Top
REF 1 Strategies for Late-Stage Optimization: Profiling Thermodynamics by Preorganization and Salt Bridge Shielding. J Med Chem. 2019 Nov 14;62(21):9753-9771.
REF 2 Thrombin Inhibition

If You Find Any Error in Data or Bug in Web Service, Please Kindly Report It to Dr. Zhou and Dr. Zhang.