4lxb.1 | SWISS-MODEL Template Library

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SMTL ID : 4lxb.1

Crystal Structure Analysis of thrombin in complex with compound D58

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.61 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 A: L.46, N.53

2 PLIP interactions:

2 interactions with chain A

Hydrophobic interactions: A:L.46
Hydrogen bonds: A:N.53

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

NA.2:	2 residues within 4Å: Chain A: R.233, K.236 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.233, A:K.236 Water bridges: A:D.234, A:G.235, A:G.238
NA.3:	2 residues within 4Å: Chain A: K.174, T.177 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.177

1 x 7R9: 5-Chloro-thiophene-2-carboxylic acid [(S)-2-[2-difluoromethoxy-3-(2-oxo-piperidin-1-yl)-benzenesulfonylamino]-3-((S)-3-dimethylamino-pyrrolidin-1-yl)-3-oxo-propyl]-amide(Non-covalent)

7R9.4:

22 residues within 4Å:

Chain A: 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, E.229, G.230, C.231, G.238, F.239, Y.240

13 PLIP interactions:

13 interactions with chain A

Hydrophobic interactions: A:W.50, A:W.50, A:L.96, A:I.179, A:A.200, A:W.227
Hydrogen bonds: A:Y.47, A:G.228, A:G.228, A:G.230, A:G.230
Water bridges: A:D.204
pi-Cation interactions: A:W.50

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Meneyrol, J. et al., 5-Chlorothiophene-2-carboxylic acid [(S)-2-[2-methyl-3-(2-oxopyrrolidin-1-yl)benzenesulfonylamino]-3-(4-methylpiperazin-1-yl)-3-oxopropyl]amide (SAR107375), a selective and potent orally active dual thrombin and factor Xa inhibitor. J.Med.Chem. (2013)

Release Date

2014-06-11

Peptides

Prothrombin, Thrombin light chain: A
Hirudin variant-1: B
Prothrombin: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
I

C
L

Export Alignment

Secondary Structure
NoneDSSPPSIPREDSSpro

Colour Scheme

Fade MismatchesEnhance Mismatches

ChainUnique ChainRainbow2° StructureBfactorBfactor RangeSOAEntropyClustalHydrophobicSizeChargedPolarProlineSer/ThrCysteineAliphaticAromaticNo Colour

Background

3D Viewer
NGLPV2D

Prothrombin, Thrombin light chain

Hirudin variant-1

Prothrombin

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