Structure of PDB 1g2l Chain A Binding Site BS02

Receptor Information
>1g2l Chain A (length=235) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
IVGGQECKDGECPWQALLINEENEGFCGGTILSEFYILTAAHCLYQAKRF
KVRVGDRNTEQEEGGEAVHEVEVVIKHNRFTKETYDFDIAVLRLKTPITF
RMNVAPACLPERDWAESTLMTQKTGIVSGFGRTHEKGRQSTRLKMLEVPY
VDRNSCKLSSSFIITQNMFCAGYDTKQEDACQGDSGGPHVTRFKDTYFVT
GIVSWGEGCARKGKYGIYTKVTAFLKWIDRSMKTR
Ligand information
Ligand IDT87
InChIInChI=1S/C29H31N7O3/c1-3-38-26(37)18-39-35-27(22-6-4-5-15-32-22)29(13-14-29)20-9-12-24-23(16-20)34-25(36(24)2)17-33-21-10-7-19(8-11-21)28(30)31/h4-12,15-16,33H,3,13-14,17-18H2,1-2H3,(H3,30,31)/b35-27-
InChIKeyRNOYCNIZOAIUSV-LSWMGQQCSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0[H]/N=C(/c1ccc(cc1)NCc2nc3cc(ccc3n2C)C4(CC4)/C(=N\OCC(=O)OCC)/c5ccccn5)\N
ACDLabs 10.04O=C(OCC)CO\N=C(\c1ncccc1)C5(c4ccc2c(nc(n2C)CNc3ccc(C(=[N@H])N)cc3)c4)CC5
CACTVS 3.341CCOC(=O)CO\N=C(c1ccccn1)/C2(CC2)c3ccc4n(C)c(CNc5ccc(cc5)C(N)=N)nc4c3
CACTVS 3.341CCOC(=O)CON=C(c1ccccn1)C2(CC2)c3ccc4n(C)c(CNc5ccc(cc5)C(N)=N)nc4c3
OpenEye OEToolkits 1.5.0[H]N=C(c1ccc(cc1)NCc2nc3cc(ccc3n2C)C4(CC4)C(=NOCC(=O)OCC)c5ccccn5)N
FormulaC29 H31 N7 O3
Name[(1-{2[(4-CARBAMIMIDOYL-PHENYLAMINO)-METHYL]-1-METHYL-1H-BENZOIMIDAZOL-5-YL}-CYCLOPROPYL)-PYRIDIN-2-YL-METHYLENEAMINOOXY]-ACETIC ACID ETHYL ESTER
ChEMBL
DrugBankDB04107
ZINCZINC000006409740
PDB chain1g2l Chain A Residue 1 [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]
PDB1g2l Structural basis for inhibition promiscuity of dual specific thrombin and factor Xa blood coagulation inhibitors.
Resolution1.9 Å
Binding residue
(original residue number in PDB)		H57 T99 Y100 F177 D194 A195 C196 Q197 S200 V218 W220 G223
Binding residue
(residue number reindexed from 1)		H42 T84 Y85 F162 D179 A180 C181 Q182 S185 V203 W205 G208
Annotation score1
Binding affinityMOAD: Ki=57nM
PDBbind-CN: -logKd/Ki=7.24,Ki=57nM
BindingDB: Ki=57nM
Enzymatic activity
Catalytic site (original residue number in PDB) H57 D103 Q197 G198 D199 S200 G201
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:1g2l, PDBe:1g2l, PDBj:1g2l
PDBsum1g2l
PubMed11342132
UniProtP00742|FA10_HUMAN Coagulation factor X (Gene Name=F10)

[Back to BioLiP]