Structure of PDB 2jkh Chain A Binding Site BS01

Receptor Information
>2jkh 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 IDBI7
InChIInChI=1S/C22H28ClN4O3S/c1-27(2,3)11-5-10-26-21(28)18-14-6-4-9-25(14)20(19(18)22(26)29)13-12-15(30-24-13)16-7-8-17(23)31-16/h7-8,12,14,18-20H,4-6,9-11H2,1-3H3/q+1/t14-,18-,19-,20-/m0/s1
InChIKeyIMQAZTOPHVBANA-DSYPUSFNSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7C[N+](C)(C)CCCN1C(=O)C2C3CCCN3C(C2C1=O)c4cc(on4)c5ccc(s5)Cl
OpenEye OEToolkits 2.0.7C[N+](C)(C)CCCN1C(=O)[C@H]2[C@@H]3CCCN3[C@H]([C@H]2C1=O)c4cc(on4)c5ccc(s5)Cl
CACTVS 3.385C[N+](C)(C)CCCN1C(=O)[CH]2[CH]3CCCN3[CH]([CH]2C1=O)c4cc(on4)c5sc(Cl)cc5
CACTVS 3.385C[N+](C)(C)CCCN1C(=O)[C@H]2[C@@H]3CCCN3[C@H]([C@H]2C1=O)c4cc(on4)c5sc(Cl)cc5
FormulaC22 H28 Cl N4 O3 S
Name3-[(3~{a}~{S},4~{R},8~{a}~{S},8~{b}~{R})-4-[5-(5-chloranylthiophen-2-yl)-1,2-oxazol-3-yl]-1,3-bis(oxidanylidene)-4,6,7,8,8~{a},8~{b}-hexahydro-3~{a}~{H}-pyrrolo[3,4-a]pyrrolizin-2-yl]propyl-trimethyl-azanium
ChEMBLCHEMBL1626802
DrugBank
ZINC
PDB chain2jkh 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

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PDB2jkh Cation-Pi Interactions at the Active Site of Factor Xa: Dramatic Enhancement Upon Stepwise N-Alkylation of Ammonium Ions.
Resolution1.25 Å
Binding residue
(original residue number in PDB)		Y99 F174 D189 A190 C191 Q192 V213 W215 G216 G226 Y228
Binding residue
(residue number reindexed from 1)		Y85 F162 D179 A180 C181 Q182 V203 W205 G206 G216 Y218
Annotation score1
Binding affinityMOAD: Ki=9nM
PDBbind-CN: -logKd/Ki=8.05,Ki=9nM
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:2jkh, PDBe:2jkh, PDBj:2jkh
PDBsum2jkh
PubMed19101972
UniProtP00742|FA10_HUMAN Coagulation factor X (Gene Name=F10)

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