Structure of PDB 4y79 Chain A Binding Site BS03

Receptor Information

>4y79 Chain A (length=234) Species: 9606 (Homo sapiens)

IVGGQECKDGECPWQALLINEENEGFCGGTILSEFYILTAAHCLYQAKRF
KVRVGDRNTEQEEGGEAVHEVEVVIKHNRFTKETYDFDIAVLRLKTPITF
RMNVAPACLPERDWAESTLMTQKTGIVSGFGRTHEKGRQSTRLKMLEVPY
VDRNSCKLSSSFIITQNMFCAGYDTKQEDACQGDSGGPHVTRFKDTYFVT
GIVSWGEGCARKGKYGIYTKVTAFLKWIDRSMKT

Ligand information

• Ligand ID: 4O6
• InChI: InChI=1S/C19H24ClN3O5S/c1-14(18(24)22-9-11-28-12-10-22)23-8-6-17(19(23)25)21-29(26,27)13-7-15-2-4-16(20)5-3-15/h2-5,7,13-14,17,21H,6,8-12H2,1H3/b13-7+/t14-,17-/m0/s1
• InChIKey: DNCVZNVETAOAJO-PPYZAHLJSA-N
• SMILES:
  OpenEye OEToolkits 1.9.2: C[C@@H](C(=O)N1CCOCC1)N2CC[C@@H](C2=O)NS(=O)(=O)/C=C/c3ccc(cc3)Cl
  ACDLabs 12.01: O=C(N1CCOCC1)C(N3C(=O)C(NS(=O)(=O)\C=C\c2ccc(Cl)cc2)CC3)C
  CACTVS 3.385: C[CH](N1CC[CH](N[S](=O)(=O)C=Cc2ccc(Cl)cc2)C1=O)C(=O)N3CCOCC3
  CACTVS 3.385: C[C@H](N1CC[C@H](N[S](=O)(=O)\C=C\c2ccc(Cl)cc2)C1=O)C(=O)N3CCOCC3
  OpenEye OEToolkits 1.9.2: CC(C(=O)N1CCOCC1)N2CCC(C2=O)NS(=O)(=O)C=Cc3ccc(cc3)Cl
• Formula: C19 H24 Cl N3 O5 S
• Name: (E)-2-(4-chlorophenyl)-N-{(3S)-1-[(2S)-1-(morpholin-4-yl)-1-oxopropan-2-yl]-2-oxopyrrolidin-3-yl}ethenesulfonamide;
  GTC000406
• ChEMBL: CHEMBL223891
• ZINC: ZINC000014965153
• PDB chain: 4y79 Chain A Residue 303

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4y79 Factor Xa inhibitors: S1 binding interactions of a series of N-{(3S)-1-[(1S)-1-methyl-2-morpholin-4-yl-2-oxoethyl]-2-oxopyrrolidin-3-yl}sulfonamides.
• Resolution: 2.1 Å
• Binding residue (original residue number in PDB): E97 T98 F174 A190 Q192 W215 G216 G219 G226 I227 Y228
• Binding residue (residue number reindexed from 1): E83 T84 F162 A180 Q182 W205 G206 G208 G216 I217 Y218
• Annotation score: 1
• Binding affinity: MOAD: Ki=11nM
  PDBbind-CN: -logKd/Ki=7.96,Ki=11nM
  BindingDB: Ki=11nM

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

External links

• PDB: RCSB:4y79, PDBe:4y79, PDBj:4y79
• PDBsum: 4y79
• PubMed: 17338508
• UniProt: P00742|FA10_HUMAN Coagulation factor X (Gene Name=F10)