SMTL ID : 2vwo.2 (2 other biounits)

Aminopyrrolidine Factor Xa inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

1 x LZG: 5-CHLORO-THIOPHENE-2-CARBOXYLIC ACID ((3S,4S)-4-FLUORO- 1-{[2-FLUORO-4-(2-OXO-2H-PYRIDIN-1-YL)-PHENYLCARBAMOYL]-METHYL}-PYRROLIDIN-3-YL)-AMIDE

LZG.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.6 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:Y.85, A:F.162, A:F.162, A:A.180, A:W.205, A:W.205 Hydrogen bonds: 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: 5 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.56, A:N.58, A:Q.61, A:E.63, A:E.66, H2O.3

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

NA.3: 4 residues within 4Å: Chain A: Y.173, D.174, R.211, K.214 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.174, A:G.213, A:K.214 NA.4: 0 residues within 4Å: (No contacts) 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.121 NA.5: 1 residues within 4Å: Chain A: Q.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.11

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

CL.6: 2 residues within 4Å: Chain A: G.208 Ligands: LZG.1 Ligand excluded by PLIP CL.7: 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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

ACTIVATED FACTOR XA HEAVY CHAIN

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