Structure of PDB 2wyg Chain A Binding Site BS01

Receptor Information

>2wyg Chain A (length=228) Species: 9606 (Homo sapiens)

IVGGQECKDGECPWQALLINEENEGFCGGTILSEFYILTAAHCLYQAKRF
KVRVGDRNTEAVHEVEVVIKHNRFTKETYDFDIAVLRLKTPITFRMNVAP
ACLPERDWAESTLMTQKTGIVSGFGRTHEKGRQSTRLKMLEVPYVDRNSC
KLSSSFIITQNMFCAGYDTKQEDACQGDSGGPHVTRFKDTYFVTGIVSWG
EGCARKGKYGIYTKVTAFLKWIDRSMKT

Ligand information

• Ligand ID: 461
• InChI: InChI=1S/C20H23ClFN3O3S2/c1-13(24(2)3)14-4-6-18(16(22)12-14)25-10-8-17(20(25)26)23-30(27,28)11-9-15-5-7-19(21)29-15/h4-7,9,11-13,17,23H,8,10H2,1-3H3/b11-9+/t13-,17+/m1/s1
• InChIKey: AFDHTIFDRFSZDA-IUJLQVPDSA-N
• SMILES:
  OpenEye OEToolkits 1.6.1: CC(c1ccc(c(c1)F)N2CCC(C2=O)NS(=O)(=O)C=Cc3ccc(s3)Cl)N(C)C
  OpenEye OEToolkits 1.6.1: C[C@H](c1ccc(c(c1)F)N2CC[C@@H](C2=O)NS(=O)(=O)\C=C\c3ccc(s3)Cl)N(C)C
  CACTVS 3.352: C[C@@H](N(C)C)c1ccc(N2CC[C@H](N[S](=O)(=O)/C=C/c3sc(Cl)cc3)C2=O)c(F)c1
  CACTVS 3.352: C[CH](N(C)C)c1ccc(N2CC[CH](N[S](=O)(=O)C=Cc3sc(Cl)cc3)C2=O)c(F)c1
  ACDLabs 10.04: Clc3sc(/C=C/S(=O)(=O)NC2C(=O)N(c1ccc(cc1F)C(N(C)C)C)CC2)cc3
• Formula: C20 H23 Cl F N3 O3 S2
• Name: (E)-2-(5-CHLOROTHIOPHEN-2-YL)-N-[(3S)-1-{4-[(1R)-1-(DIMETHYLAMINO)ETHYL]-2-FLUOROPHENYL}-2-OXOPYRROLIDIN-3-YL]ETHENESULFONAMIDE
• ChEMBL: CHEMBL593584
• ZINC: ZINC000038336010
• PDB chain: 2wyg Chain A Residue 1245

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2wyg Structure and Property Based Design of Factor Xa Inhibitors: Pyrrolidin-2-Ones with Monoaryl P4 Motifs
• Resolution: 1.88 Å
• Binding residue (original residue number in PDB): E97 Y99 F174 D189 A190 Q192 V213 W215 G216 G226 I227 Y228
• Binding residue (residue number reindexed from 1): E77 Y79 F156 D173 A174 Q176 V197 W199 G200 G210 I211 Y212
• Annotation score: 1
• Binding affinity: MOAD: Ki=2nM
  PDBbind-CN: -logKd/Ki=8.70,Ki=2nM
  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 D82 Q176 G177 D178 S179 G180
• 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

External links

• PDB: RCSB:2wyg, PDBe:2wyg, PDBj:2wyg
• PDBsum: 2wyg
• PubMed: 20006499
• UniProt: P00742|FA10_HUMAN Coagulation factor X (Gene Name=F10)