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SMTL ID : 3qx5.1

Thrombin Inhibition by Pyridin Derivatives

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.35 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 B: L.46, N.53

2 PLIP interactions:

2 interactions with chain B

Hydrophobic interactions: B:L.46
Water bridges: B:N.53

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

NA.2:	3 residues within 4Å: Chain B: K.174, D.175, T.177 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.174
NA.3:	2 residues within 4Å: Chain B: R.233, K.236 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.236, B:K.236 Water bridges: B:G.235, B:G.238

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.4:

4 residues within 4Å:

Chain B: N.91, D.97, R.98, R.180

8 PLIP interactions:

8 interactions with chain B

Hydrogen bonds: B:N.91, B:D.97
Water bridges: B:R.89, B:R.180, B:R.180, B:R.180
Salt bridges: B:R.98, B:R.180

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.5:

7 residues within 4Å:

Chain B: L.27, C.28, W.50, K.52, E.202, G.203, S.205

4 PLIP interactions:

4 interactions with chain B

Hydrogen bonds: B:L.27, B:K.52, B:G.203, B:S.205

1 x 02P: D-phenylalanyl-N-[(4-chloro-1-methylpyridinium-2-yl)methyl]-L-prolinamide(Non-covalent)

02P.6:

17 residues within 4Å:

Chain B: H.43, Y.47, W.50, E.94, N.95, I.179, D.199, A.200, S.205, V.225, S.226, W.227, G.228, G.230, G.238, F.239, Y.240

9 PLIP interactions:

9 interactions with chain B

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

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Biela, A. et al., Impact of ligand and protein desolvation on ligand binding to the S1 pocket of thrombin. J.Mol.Biol. (2012)

Release Date

2012-03-07

Peptides

Thrombin light chain: A
Thrombin heavy chain: 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

Thrombin light chain

Thrombin heavy chain

Hirudin variant-2

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1a2c.1 | 1a3b.1 | 1a3e.1 | 1a46.1 | 1a4w.1 | 1a5g.1 | 1a61.1 | 1abi.1 | 1abj.1 | 1ad8.1 | 1ae8.1 | 1afe.1 | 1aht.1 | 1ai8.1 | 1aix.1 | 1awf.1 | 1awh.1 | 1awh.2 | 1ay6.1 | 1b5g.1 | 1b7x.1 | 1ba8.1 | 1bb0.1 | 1bcu.1 | 1bmm.1 | 1bmn.1 | 1bth.1 | 1bth.2 | 1c1u.1 | 1c1v.1 more...less...

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