Structure of PDB 2y82 Chain A Binding Site BS01

Receptor Information
>2y82 Chain A (length=234) 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
GIVSWGEGCARKGKYGIYTKVTAFLKWIDRSMKT
Ligand information
Ligand ID930
InChIInChI=1S/C24H23ClFN3O3S/c25-18-6-3-16-13-19(7-4-15(16)12-18)33(31,32)28-22-9-11-29(24(22)30)23-8-5-17(14-20(23)26)21-2-1-10-27-21/h3-8,12-14,21-22,27-28H,1-2,9-11H2/t21-,22-/m0/s1
InChIKeyOKMBULRSJZKGQF-VXKWHMMOSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.6.1c1cc(cc2c1cc(cc2)Cl)S(=O)(=O)N[C@H]3CCN(C3=O)c4ccc(cc4F)[C@@H]5CCCN5
OpenEye OEToolkits 1.6.1c1cc(cc2c1cc(cc2)Cl)S(=O)(=O)NC3CCN(C3=O)c4ccc(cc4F)C5CCCN5
CACTVS 3.352Fc1cc(ccc1N2CC[CH](N[S](=O)(=O)c3ccc4cc(Cl)ccc4c3)C2=O)[CH]5CCCN5
CACTVS 3.352Fc1cc(ccc1N2CC[C@H](N[S](=O)(=O)c3ccc4cc(Cl)ccc4c3)C2=O)[C@@H]5CCCN5
FormulaC24 H23 Cl F N3 O3 S
Name6-CHLORO-N-((3S)-2-OXO-1-{4-[(2S)-2-PYRROLIDINYL]PHENYL}-3-PYRROLIDINYL)-2-NAPHTHALENESULFONAMIDE
ChEMBLCHEMBL1614818
DrugBank
ZINCZINC000064744333
PDB chain2y82 Chain A Residue 1245 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2y82 Structure and Property Based Design of Factor Xa Inhibitors: Pyrrolidin-2-Ones with Aminoindane and Phenylpyrrolidine P4 Motifs.
Resolution2.2 Å
Binding residue
(original residue number in PDB)		E97 T98 Y99 F174 D189 A190 Q192 V213 W215 G216 G219 C220 G226 I227 Y228
Binding residue
(residue number reindexed from 1)		E83 T84 Y85 F162 D179 A180 Q182 V203 W205 G206 G208 C209 G216 I217 Y218
Annotation score1
Binding affinityMOAD: Ki=4nM
PDBbind-CN: -logKd/Ki=8.40,Ki=4nM
BindingDB: Ki=2nM
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:2y82, PDBe:2y82, PDBj:2y82
PDBsum2y82
PubMed21349710
UniProtP00742|FA10_HUMAN Coagulation factor X (Gene Name=F10)

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