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SMTL ID : 1d4p.1

CRYSTAL STRUCTURE OF HUMAN ALPHA THROMBIN IN COMPLEX WITH 5-AMIDINOINDOLE-4-BENZYLPIPERIDINE INHIBITOR

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.07 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

1 PLIP interactions:

1 interactions with chain B

Hydrophobic interactions: B:L.46

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

NA.2:	2 residues within 4Å: Chain B: K.174, T.177 3 PLIP interactions: 3 interactions with chain B Water bridges: B:K.174, B:D.175, B:R.178
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:R.233, B:K.236 Water bridges: B:G.235, B:G.238

1 x BPP: 2-(4-benzylpiperidine-1-carbonyl)-1H-indole-5-carboximidamide(Non-covalent)

BPP.4:

16 residues within 4Å:

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

12 PLIP interactions:

12 interactions with chain B

Hydrophobic interactions: B:Y.47, B:W.50, B:L.96, B:V.225, B:W.227, B:W.227
Hydrogen bonds: B:D.199, B:A.200, B:G.230
Water bridges: B:H.43, B:G.203, B:F.239

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Chirgadze, N.Y. et al., The crystal structure of human alpha-thrombin complexed with LY178550, a nonpeptidyl, active site-directed inhibitor. Protein Sci. (1997)

Release Date

1999-10-20

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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