Structure of PDB 1g2m Chain A Binding Site BS02

Receptor Information
>1g2m 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 IDR11
InChIInChI=1S/C25H25N7/c1-16-29-20-5-3-4-6-23(20)32(16)15-17-7-12-22-21(13-17)30-24(31(22)2)14-28-19-10-8-18(9-11-19)25(26)27/h3-13,28H,14-15H2,1-2H3,(H3,26,27)
InChIKeyIRKPNOLLMNHSOU-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341Cn1c(CNc2ccc(cc2)C(N)=N)nc3cc(Cn4c(C)nc5ccccc45)ccc13
OpenEye OEToolkits 1.5.0[H]/N=C(/c1ccc(cc1)NCc2nc3cc(ccc3n2C)Cn4c(nc5c4cccc5)C)\N
ACDLabs 10.04[N@H]=C(N)c1ccc(cc1)NCc3nc2cc(ccc2n3C)Cn4c5ccccc5nc4C
OpenEye OEToolkits 1.5.0[H]N=C(c1ccc(cc1)NCc2nc3cc(ccc3n2C)Cn4c(nc5c4cccc5)C)N
FormulaC25 H25 N7
Name4-{[1-METHYL-5-(2-METHYL-BENZOIMIDAZOL-1-YLMETHYL)-1H-BENZOIMIDAZOL-2-YLMETHYL]-AMINO}-BENZAMIDINE
ChEMBL
DrugBankDB02354
ZINCZINC000000591050
PDB chain1g2m Chain A Residue 1 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1g2m Structural basis for inhibition promiscuity of dual specific thrombin and factor Xa blood coagulation inhibitors.
Resolution3.02 Å
Binding residue
(original residue number in PDB)		H57 T98 Y99 F174 D189 A190 C191 V213 W215 G216 G218 C220
Binding residue
(residue number reindexed from 1)		H42 T84 Y85 F162 D179 A180 C181 V203 W205 G206 G208 C209
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=7.40,Ki=40nM
BindingDB: Ki=40nM
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

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Molecular Function
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Biological Process
External links
PDB RCSB:1g2m, PDBe:1g2m, PDBj:1g2m
PDBsum1g2m
PubMed11342132
UniProtP00742|FA10_HUMAN Coagulation factor X (Gene Name=F10)

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