Structure of PDB 3k9x Chain A Binding Site BS01

Receptor Information

>3k9x Chain A (length=86) Species: 9606 (Homo sapiens)

CETSPCQNQGKCKDEYTCTCLEGFEGKNCELFTRKLCSLDNGDCDQFCHE
EQNSVVCSCARGYTLADNGKACIPTGPYPCGKQTLE

Ligand information

• Ligand ID: MBM
• InChI: InChI=1S/C28H32N6O4/c1-19-15-21-16-22(9-10-24(21)38-19)30-28(32-26(36)20-7-6-11-29-17-20)31-23-8-2-3-14-34(27(23)37)18-25(35)33-12-4-5-13-33/h6-7,9-11,15-17,23H,2-5,8,12-14,18H2,1H3,(H2,30,31,32,36)/t23-/m0/s1
• InChIKey: GNYXHJVKEWBHAI-QHCPKHFHSA-N
• SMILES:
  CACTVS 3.352: Cc1oc2ccc(cc2c1)N=C(N[C@H]3CCCCN(CC(=O)N4CCCC4)C3=O)NC(=O)c5cccnc5
  ACDLabs 11.02: O=C2N(CC(=O)N1CCCC1)CCCCC2N/C(=N\c4cc3c(oc(c3)C)cc4)NC(=O)c5cccnc5
  OpenEye OEToolkits 1.7.0: Cc1cc2cc(ccc2o1)N=C(NC3CCCCN(C3=O)CC(=O)N4CCCC4)NC(=O)c5cccnc5
  OpenEye OEToolkits 1.7.0: Cc1cc2cc(ccc2o1)/N=C(\N[C@H]3CCCCN(C3=O)CC(=O)N4CCCC4)/NC(=O)c5cccnc5
  CACTVS 3.352: Cc1oc2ccc(cc2c1)N=C(N[CH]3CCCCN(CC(=O)N4CCCC4)C3=O)NC(=O)c5cccnc5
• Formula: C28 H32 N6 O4
• Name: N-{N'-(2-methyl-1-benzofuran-5-yl)-N-[(3S)-2-oxo-1-(2-oxo-2-pyrrolidin-1-ylethyl)azepan-3-yl]carbamimidoyl}pyridine-3-carboxamide
• ChEMBL: CHEMBL567904
• ZINC: ZINC000044460288
• PDB chain: 3k9x Chain D Residue 2

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3k9x Aroylguanidine-based factor Xa inhibitors: the discovery of BMS-344577
• Resolution: 1.9 Å
• Binding residue (original residue number in PDB): Q96 N120
• Binding residue (residue number reindexed from 1): Q7 N28
• Annotation score: 1
• Binding affinity: BindingDB: IC50=4nM

Enzymatic activity

• Enzyme Commision number: 3.4.21.6: coagulation factor Xa.

Gene Ontology

Molecular Function

• GO:0005509 calcium ion binding

External links

• PDB: RCSB:3k9x, PDBe:3k9x, PDBj:3k9x
• PDBsum: 3k9x
• PubMed: 19896847
• UniProt: P00742|FA10_HUMAN Coagulation factor X (Gene Name=F10)