Structure of PDB 2y80 Chain B Binding Site BS01

Receptor Information

>2y80 Chain B (length=52) Species: 9606 (Homo sapiens)

RKLCSLDNGDCDQFCHEEQNSVVCSCARGYTLADNGKACIPTGPYPCGKQ
TL

Ligand information

• Ligand ID: 439
• InChI: InChI=1S/C25H26ClN3O3S/c1-28(2)24-10-5-18-14-20(7-9-22(18)24)29-12-11-23(25(29)30)27-33(31,32)21-8-4-16-13-19(26)6-3-17(16)15-21/h3-4,6-9,13-15,23-24,27H,5,10-12H2,1-2H3/t23-,24+/m0/s1
• InChIKey: DBFTVRMJVISJEX-BJKOFHAPSA-N
• SMILES:
  OpenEye OEToolkits 1.6.1: CN(C)C1CCc2c1ccc(c2)N3CCC(C3=O)NS(=O)(=O)c4ccc5cc(ccc5c4)Cl
  CACTVS 3.352: CN(C)[CH]1CCc2cc(ccc12)N3CC[CH](N[S](=O)(=O)c4ccc5cc(Cl)ccc5c4)C3=O
  OpenEye OEToolkits 1.6.1: CN(C)[C@@H]1CCc2c1ccc(c2)N3CC[C@@H](C3=O)NS(=O)(=O)c4ccc5cc(ccc5c4)Cl
  CACTVS 3.352: CN(C)[C@@H]1CCc2cc(ccc12)N3CC[C@H](N[S](=O)(=O)c4ccc5cc(Cl)ccc5c4)C3=O
• Formula: C25 H26 Cl N3 O3 S
• Name: 6-CHLORO-N-{(3S)-1-[(1S)-1-(DIMETHYLAMINO)-2,3-DIHYDRO-1H-INDEN-5-YL]-2-OXO-3-PYRROLIDINYL}-2-NAPHTHALENESULFONAMIDE
• ChEMBL: CHEMBL1614790
• ZINC: ZINC000035834638
• PDB chain: 2y80 Chain A Residue 1245

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2y80 Structure and Property Based Design of Factor Xa Inhibitors: Pyrrolidin-2-Ones with Aminoindane and Phenylpyrrolidine P4 Motifs.
• Resolution: 1.9 Å
• Binding residue (original residue number in PDB): T48 L49
• Binding residue (residue number reindexed from 1): T51 L52
• Annotation score: 1
• Binding affinity: BindingDB: Ki=3nM

Enzymatic activity

• Enzyme Commision number: 3.4.21.6: coagulation factor Xa.

Gene Ontology

Molecular Function

• GO:0005509 calcium ion binding

Cellular Component

• GO:0005576 extracellular region

External links

• PDB: RCSB:2y80, PDBe:2y80, PDBj:2y80
• PDBsum: 2y80
• PubMed: 21349710
• UniProt: P00742|FA10_HUMAN Coagulation factor X (Gene Name=F10)