SMTL ID : 3dux.1

Understanding Thrombin Inhibition

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x 64U: 3-cyclohexyl-D-alanyl-N-(3-chlorobenzyl)-L-prolinamide(Non-covalent)

64U.1: 16 residues within 4Å: Chain B: H.43, Y.47, W.50, E.94, N.95, D.199, A.200, C.201, S.205, V.225, S.226, W.227, G.228, G.230, G.238, F.239 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:Y.47, B:W.50, B:A.200, B:V.225, B:W.227 Hydrogen bonds: B:S.226, B:G.228 pi-Stacking: B:H.43

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

NA.2: 2 residues within 4Å: Chain B: R.233, K.236 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.236, B:K.236 Water bridges: B:G.238 NA.3: 1 residues within 4Å: Chain B: F.215 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Baum, B. et al., Think twice: understanding the high potency of bis(phenyl)methane inhibitors of thrombin. J.Mol.Biol. (2009)

Release Date

2009-06-23

Peptides

Thrombin Light Chain: A
Thrombin Heavy Chain: B
Hirudin variant-1: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
L

B
H

C
I

Thrombin Light Chain

Thrombin Heavy Chain

Hirudin variant-1

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