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SMTL ID : 1d3p.1

CRYSTAL STRUCTURE OF HUMAN APLHA-THROMBIN IN COMPLEX WITH BENZO[B]THIOPHENE INHIBITOR 3

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

NAG.1:

3 residues within 4Å:

Chain B: L.46, 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 2 PLIP interactions: 2 interactions with chain B Water bridges: B:K.174, B:D.175
NA.3:	2 residues within 4Å: Chain B: R.233, K.236 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:K.236, B:K.236 Water bridges: B:D.232, B:R.233, B:G.235

1 x BT3: 3-[4-(2-PYRROLIDIN-1-YL-ETHOXY)-BENZYL]-2-4-(2-PYRROLIDIN-1-YL-ETHOXY)-PHENYL] -BENZO[B]THIOPHEN-6-OL(Non-covalent)

BT3.4:

19 residues within 4Å:

Chain B: H.43, Y.47, W.50, E.94, N.95, L.96, I.179, D.199, A.200, C.201, E.202, S.205, V.225, S.226, W.227, G.228, G.230, C.231, G.238

14 PLIP interactions:

14 interactions with chain B

Hydrophobic interactions: B:W.50, B:W.50, B:L.96, B:L.96, B:E.202, B:V.225, B:W.227, B:W.227
Hydrogen bonds: B:D.199
Water bridges: B:E.202, B:G.238
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

Export Alignment

Secondary Structure
NoneDSSPPSIPREDSSpro

Colour Scheme

Fade MismatchesEnhance Mismatches

ChainUnique ChainRainbow2° StructureBfactorBfactor RangeSOAEntropyClustalHydrophobicSizeChargedPolarProlineSer/ThrCysteineAliphaticAromaticNo Colour

Background

3D Viewer
NGLPV2D

ALPHA-THROMBIN

ALPHA-THROMBIN

HIRUGEN

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