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SMTL ID : 3dhk.1

Bisphenylic Thrombin Inhibitors

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.73 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x 23U: beta-phenyl-D-phenylalanyl-N-(3-chlorobenzyl)-L-prolinamide(Non-covalent)

23U.1:

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, S.205, V.225, S.226, W.227, G.228, E.229, G.230, G.238, F.239

14 PLIP interactions:

14 interactions with chain B

Hydrophobic interactions: B:Y.47, B:W.50, B:L.96, B:L.96, B:I.179, B:A.200, B:V.225, B:W.227, B:E.229, B:E.229
Hydrogen bonds: B:S.226, B:G.228
Water bridges: B:G.228, B:G.230

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

NA.2:	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:G.235, B:G.238
NA.3:	2 residues within 4Å: Chain B: K.174, T.177 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.174, B:T.177

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

2009-05-19

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

Export Alignment

Secondary Structure
NoneDSSPPSIPREDSSpro

Colour Scheme

Fade MismatchesEnhance Mismatches

ChainUnique ChainRainbow2° StructureBfactorBfactor RangeSOAEntropyClustalHydrophobicSizeChargedPolarProlineSer/ThrCysteineAliphaticAromaticNo Colour

Background

3D Viewer
NGLPV2D

Thrombin light chain

Thrombin heavy chain

Hirudin variant-1

Related Entries With Identical Sequence

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