SMTL ID : 1d3d.1

CRYSTAL STRUCTURE OF HUMAN ALPHA THROMBIN IN COMPLEX WITH BENZOTHIOPHENE INHIBITOR 4

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.04 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.1: 2 residues within 4Å: Chain B: N.53, T.55 No protein-ligand interaction detected (PLIP)

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

NA.2: 2 residues within 4Å: Chain B: K.174, T.177 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.174 NA.3: 3 residues within 4Å: Chain B: D.232, R.233, K.236 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.236, B:K.236 Water bridges: B:R.197, B:G.238

1 x BZT: 3-(3-BROMO-4-PYRROLIDIN-1-YLMETHYL-BENZYL)-2-[4-PYRROLIDIN-1-YL-ETHOXY)-PHENYL]-BENZO[B]THIOPHEN-6-OL(Non-covalent)

BZT.4: 16 residues within 4Å: Chain B: H.43, Y.47, W.50, L.96, I.179, D.199, A.200, C.201, E.202, S.205, V.225, S.226, W.227, G.228, C.231, G.238 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:W.50, B:W.50, B:I.179, B:E.202, B:V.225 Hydrogen bonds: B:D.199, B:A.200 Water bridges: B:G.238 Salt bridges: B:E.202 pi-Stacking: B:H.43 pi-Cation interactions: B:W.50, B:W.50

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chirgadze, N.Y. et al., The crystal structures of human alpha-thrombin complexed with active site-directed diamino benzo[b]thiophene derivatives: a binding mode for a structurally novel class of inhibitors. Protein Sci. (2000)

Release Date

2000-10-04

Peptides

ALPHA-THROMBIN: A
ALPHA-THROMBIN: B
HIRUGEN: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
H

ALPHA-THROMBIN

ALPHA-THROMBIN

HIRUGEN

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