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SMTL ID : 6eo9.1

Crystal structure of thrombin in complex with a novel glucose-conjugated potent inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.84 Å

Oligo State

hetero-1-1-1-mer

Ligands

6 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.1:	8 residues within 4Å: Chain A: E.3, S.5, V.162, V.163, N.164, K.196 Chain B: T.24, E.27 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:N.164, A:K.196 Salt bridges: B:E.27
DMS.2:	2 residues within 4Å: Chain A: T.182, D.183 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.183 Salt bridges: A:D.183
DMS.3:	4 residues within 4Å: Chain A: R.98, N.184, R.245, L.246 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.98 Water bridges: A:R.98
DMS.4:	4 residues within 4Å: Chain A: L.130, I.167, R.170, F.186 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.170
DMS.5:	4 residues within 4Å: Chain A: S.128, Y.134, F.215 Chain B: Y.32 No protein-ligand interaction detected (PLIP)
DMS.6:	7 residues within 4Å: Chain A: H.43, Y.47, W.50, L.96, S.226, W.227 Ligands: 2OJ.7 1 PLIP interactions: 1 interactions with chain A pi-Cation interactions: A:H.43

1 x 2OJ: N-(2-{[5-(5-chlorothiophen-2-yl)-1,2-oxazol-3-yl]methoxy}-6-{3-[(2,3,4,6-tetra-O-acetyl-beta-D-glucopyranosyl)oxy]propoxy}phenyl)-1-(propan-2-yl)piperidine-4-carboxamide(Non-covalent)

2OJ.7:

16 residues within 4Å:

Chain A: Y.47, E.94, I.179, D.199, A.200, C.201, E.202, V.225, W.227, G.228, E.229, G.230, G.238, F.239, Y.240
Ligands: DMS.6

4 PLIP interactions:

4 interactions with chain A

Hydrophobic interactions: A:I.179, A:A.200, A:W.227
Hydrogen bonds: A:G.228

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Belviso, B.D. et al., How a beta-D-glucoside side chain enhances binding affinity to thrombin of inhibitors bearing 2-chlorothiophene as P1 moiety: crystallography, fragment deconstruction study, and evaluation of antithrombotic properties. J. Med. Chem. (2014)

Release Date

2017-12-13

Peptides

Prothrombin: A
Prothrombin: B
Hirudin variant-2: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
L

C
I

Export Alignment

Secondary Structure
NoneDSSPPSIPREDSSpro

Colour Scheme

Fade MismatchesEnhance Mismatches

ChainUnique ChainRainbow2° StructureBfactorBfactor RangeSOAEntropyClustalHydrophobicSizeChargedPolarProlineSer/ThrCysteineAliphaticAromaticNo Colour

Background

3D Viewer
NGLPV2D

Prothrombin

Prothrombin

Hirudin variant-2

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