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SMTL ID : 6eo8.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.94 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

DMS.1:	6 residues within 4Å: Chain A: T.24 Chain B: S.5, V.162, V.163, N.164, K.196 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:N.164, B:K.196 Salt bridges: A:E.27
DMS.2:	1 residues within 4Å: Chain B: R.245 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.245
DMS.3:	2 residues within 4Å: Chain B: T.182, D.183 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:D.183
DMS.4:	6 residues within 4Å: Chain B: L.130, A.132, I.167, V.168, R.170, F.186 No protein-ligand interaction detected (PLIP)
DMS.5:	8 residues within 4Å: Chain B: H.43, Y.47, W.50, L.96, S.205, S.226, W.227 Ligands: 2FN.7 2 PLIP interactions: 2 interactions with chain B pi-Cation interactions: B:H.43, B:Y.47
DMS.6:	2 residues within 4Å: Chain B: S.176, K.236 No protein-ligand interaction detected (PLIP)

1 x 2FN: N-(2-{[5-(5-chlorothiophen-2-yl)-1,2-oxazol-3-yl]methoxy}-6-[3-(beta-D-glucopyranosyloxy)propoxy]phenyl)-1-(propan-2-yl)piperidine-4-carboxamide(Non-covalent)

2FN.7:

21 residues within 4Å:

Chain B: Y.47, W.50, E.94, I.179, D.199, A.200, C.201, E.202, V.225, S.226, W.227, G.228, E.229, G.230, C.231, R.233, K.236, G.238, F.239, Y.240
Ligands: DMS.5

13 PLIP interactions:

13 interactions with chain B

Hydrophobic interactions: B:W.50, B:I.179, B:A.200, B:W.227, B:E.229
Hydrogen bonds: B:G.228, B:E.229, B:G.230, B:K.236
Water bridges: B:G.228, B:R.233, B:R.233
Salt bridges: B:R.233

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
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

Prothrombin

Prothrombin

Hirudin variant-2

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