Structure of PDB 2vvu Chain A Binding Site BS01

Receptor Information
>2vvu Chain A (length=233) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
IVGGQECKDGECPWQALLINEENEGFCGGTILSEFYILTAAHCLYQAKRF
KVRVGDRNTEQEEGGEAVHEVEVVIKHNRFTKETYDFDIAVLRLKTPITF
RMNVAPACLPERDWAESTLMTQKTGIVSGFGRTHEKGEQSTRLKMLEVPY
VDRNSCKLSSSFIITQNMFCAGYDTKQEDACQGDSGGPHVTRFKDTYFVT
GIVSWGEGCARKGKYGIYTKVTAFLKWIDRSMK
Ligand information
Ligand IDH22
InChIInChI=1S/C22H20ClFN4O3S/c23-19-7-6-18(32-19)22(31)25-14-8-10-27(12-14)13-20(29)26-17-5-4-15(11-16(17)24)28-9-2-1-3-21(28)30/h1-7,9,11,14H,8,10,12-13H2,(H,25,31)(H,26,29)/t14-/m1/s1
InChIKeyIYGIXVNAMZPBDK-CQSZACIVSA-N
SMILES
SoftwareSMILES
CACTVS 3.341Fc1cc(ccc1NC(=O)CN2CC[C@H](C2)NC(=O)c3sc(Cl)cc3)N4C=CC=CC4=O
CACTVS 3.341Fc1cc(ccc1NC(=O)CN2CC[CH](C2)NC(=O)c3sc(Cl)cc3)N4C=CC=CC4=O
ACDLabs 10.04O=C(NC3CCN(CC(=O)Nc2ccc(N1C=CC=CC1=O)cc2F)C3)c4sc(Cl)cc4
OpenEye OEToolkits 1.5.0c1cc(c(cc1N2C=CC=CC2=O)F)NC(=O)CN3CCC(C3)NC(=O)c4ccc(s4)Cl
OpenEye OEToolkits 1.5.0c1cc(c(cc1N2C=CC=CC2=O)F)NC(=O)C[N@@]3CC[C@H](C3)NC(=O)c4ccc(s4)Cl
FormulaC22 H20 Cl F N4 O3 S
Name5-chloro-N-[(3R)-1-(2-{[2-fluoro-4-(2-oxopyridin-1(2H)-yl)phenyl]amino}-2-oxoethyl)pyrrolidin-3-yl]thiophene-2-carboxamide
ChEMBLCHEMBL557915
DrugBankDB07872
ZINCZINC000043019461
PDB chain2vvu Chain A Residue 1244 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB2vvu Design of Novel Aminopyrrolidine Factor Xa Inhibitors from a Screening Hit.
Resolution2.3 Å
Binding residue
(original residue number in PDB)		E97 T98 Y99 F174 D189 A190 V213 W215 G216 G218 C220 G226 I227 Y228
Binding residue
(residue number reindexed from 1)		E83 T84 Y85 F162 D179 A180 V203 W205 G206 G208 C209 G216 I217 Y218
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=8.10,Ki=8nM
BindingDB: Ki=8nM
Enzymatic activity
Catalytic site (original residue number in PDB) H57 D102 Q192 G193 D194 S195 G196
Catalytic site (residue number reindexed from 1) H42 D88 Q182 G183 D184 S185 G186
Enzyme Commision number 3.4.21.6: coagulation factor Xa.
Gene Ontology
Molecular Function
GO:0004252 serine-type endopeptidase activity
Biological Process
GO:0006508 proteolysis

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:2vvu, PDBe:2vvu, PDBj:2vvu
PDBsum2vvu
PubMed19200624
UniProtP00742|FA10_HUMAN Coagulation factor X (Gene Name=F10)

[Back to BioLiP]