SMTL ID : 2xbv.1

Factor Xa in complex with a pyrrolidine-3,4-dicarboxylic acid inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.66 Å

Oligo State

hetero-1-1-mer

Ligands

1 x XBV: (3R,4R)-1-(2,2-DIFLUORO-ETHYL)-PYRROLIDINE-3,4-DICARBOXYLIC ACID 3-[(5-CHLORO-PYRIDIN-2-YL)-AMIDE]-4-{[2-FLUORO-4-(2-OXO-2H-PYRIDIN-1-YL)-PHENYL]-AMIDE}(Non-covalent)

XBV.1: 19 residues within 4Å: Chain A: K.82, E.83, T.84, Y.85, R.132, E.135, F.162, D.179, A.180, C.181, Q.182, V.203, W.205, G.206, G.208, C.209, G.216, I.217, Y.218 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:Y.85, A:F.162, A:F.162, A:W.205, A:W.205 Hydrogen bonds: A:G.206, A:G.208 Water bridges: A:Q.182 pi-Stacking: A:Y.85, A:F.162, A:W.205, A:W.205 Halogen bonds: A:Q.182

1 x CA: CALCIUM ION(Non-covalent)

CA.2: 5 residues within 4Å: Chain A: D.56, N.58, Q.61, E.63, E.66 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.56, A:N.58, A:Q.61, A:E.66, H2O.4, H2O.4

1 x NA: SODIUM ION(Non-functional Binders)

NA.3: 5 residues within 4Å: Chain A: Y.173, D.174, A.210, R.211, K.214 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.173, A:K.214

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Anselm, L. et al., Discovery of a Factor Xa Inhibitor (3R,4R)-1-(2,2-Difluoro-Ethyl)-Pyrrolidine-3,4-Dicarboxylic Acid 3-[(5-Chloro-Pyridin-2-Yl)-Amide] 4-{[2-Fluoro-4-(2-Oxo-2H-Pyridin-1-Yl)-Phenyl]-Amide} as a Clinical Candidate. Bioorg.Med.Chem. (2010)

Release Date

2010-08-04

Peptides

ACTIVATED FACTOR XA HEAVY CHAIN: A
FACTOR X LIGHT CHAIN: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
L

ACTIVATED FACTOR XA HEAVY CHAIN

FACTOR X LIGHT CHAIN

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