SMTL ID : 2vwn.1 (2 other biounits)

Aminopyrrolidine Factor Xa inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.61 Å

Oligo State

hetero-1-1-mer

Ligands

1 x H25: 5-Chloro-thiophene-2-carboxylic acid ((3S,4S)-1-{[2-fluoro-4-(2-oxo-2H-pyridin-1-yl)-phenylcarbamoyl]-methyl}-4-hydroxy-pyrrolidin-3-yl)-amide

H25.1: 19 residues within 4Å: Chain A: K.82, E.83, T.84, Y.85, F.162, D.179, A.180, C.181, Q.182, S.185, V.203, W.205, G.206, G.208, C.209, G.216, I.217, Y.218 Ligands: CL.4 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:Q.182, A:G.206, A:G.208 Water bridges: A:S.185 pi-Stacking: A:Y.85, A:F.162, A:W.205, A:W.205

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.3, H2O.3

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

NA.3: 4 residues within 4Å: Chain A: Y.173, D.174, R.211, K.214 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.174, A:K.214 NA.6: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 2 residues within 4Å: Chain A: G.208 Ligands: H25.1 Ligand excluded by PLIP CL.5: 2 residues within 4Å: Chain A: T.165, Q.166 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zbinden, K.G. et al., Design of Novel Aminopyrrolidine Factor Xa Inhibitors from a Screening Hit. Eur.J.Med.Chem. (2009)

Release Date

2009-07-07

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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