Structure of PDB 2y5g Chain A Binding Site BS01

Receptor Information
>2y5g 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 IDFJD
InChIInChI=1S/C22H28ClN4O3S/c1-27(2,3)11-5-10-26-21(28)17-13-6-4-9-25(13)19(18(17)22(26)29)20-24-12-14(30-20)15-7-8-16(23)31-15/h7-8,12-13,17-19H,4-6,9-11H2,1-3H3/q+1/t13-,17-,18-,19+/m0/s1
InChIKeyAYOZEWNCAPQIAE-ZQEOTTOMSA-N
SMILES
SoftwareSMILES
CACTVS 3.352C[N+](C)(C)CCCN1C(=O)[C@H]2[C@@H]3CCCN3[C@H]([C@H]2C1=O)c4oc(cn4)c5sc(Cl)cc5
CACTVS 3.352C[N+](C)(C)CCCN1C(=O)[CH]2[CH]3CCCN3[CH]([CH]2C1=O)c4oc(cn4)c5sc(Cl)cc5
OpenEye OEToolkits 1.6.1C[N+](C)(C)CCCN1C(=O)C2C3CCCN3C(C2C1=O)c4ncc(o4)c5ccc(s5)Cl
OpenEye OEToolkits 1.6.1C[N+](C)(C)CCCN1C(=O)[C@H]2[C@@H]3CCC[N@@]3[C@H]([C@H]2C1=O)c4ncc(o4)c5ccc(s5)Cl
FormulaC22 H28 Cl N4 O3 S
Name3-[(3AS,4R,5S,8AS,8BR)-4-[5-(5-CHLOROTHIOPHEN-2-YL)-1,3-OXAZOL-2-YL]-1,3-DIOXO-4,6,7,8,8A,8B-HEXAHYDRO-3AH-PYRROLO[3,4-A]PYRROLIZIN-2-YL]PROPYL-TRIMETHYL-AZANIUM
ChEMBLCHEMBL4283525
DrugBank
ZINCZINC000095920597
PDB chain2y5g Chain A Residue 1244 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2y5g Molecular Recognition at the Active Site of Factor Xa: Cation-Pi Interactions, Stacking on Planar Peptide Surfaces, and Replacement of Structural Water.
Resolution1.29 Å
Binding residue
(original residue number in PDB)		T98 Y99 F174 D189 A190 Q192 V213 W215 G216 G218 G226 I227 Y228
Binding residue
(residue number reindexed from 1)		T84 Y85 F162 D179 A180 Q182 V203 W205 G206 G208 G216 I217 Y218
Annotation score1
Binding affinityMOAD: Ki=146nM
PDBbind-CN: -logKd/Ki=6.84,Ki=146nM
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:2y5g, PDBe:2y5g, PDBj:2y5g
PDBsum2y5g
PubMed22162109
UniProtP00742|FA10_HUMAN Coagulation factor X (Gene Name=F10)

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