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SMTL ID : 4yes.1

Thrombin in complex with (S)-(4-chloro-2-((1-(5-methyl-1H-pyrrole-2-carbonyl)pyrrolidine-2-carboxamido)methyl)phenyl)methanaminium

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1:

2 residues within 4Å:

Chain B: R.233, K.236

5 PLIP interactions:

2 interactions with chain B, 3 Ligand-Water interactions

Metal complexes: B:R.233, B:K.236, H₂O.4, H₂O.5, H₂O.8

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.2:

4 residues within 4Å:

Chain B: R.98, N.184, R.245, L.246

2 PLIP interactions:

2 interactions with chain B

Hydrogen bonds: B:R.98
Water bridges: B:H.87

1 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.3:

3 residues within 4Å:

Chain B: L.46, P.48, N.53

3 PLIP interactions:

3 interactions with chain B

Hydrophobic interactions: B:L.46, B:P.48
Hydrogen bonds: B:N.53

1 x 45S: N-[2-(aminomethyl)-5-chlorobenzyl]-1-[(5-methyl-1H-pyrrol-2-yl)carbonyl]-L-prolinamide(Non-covalent)

45S.4:

19 residues within 4Å:

Chain B: H.43, Y.47, W.50, 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

10 PLIP interactions:

10 interactions with chain B

Hydrophobic interactions: B:Y.47, B:W.50, B:I.179, B:V.225, B:E.229
Hydrogen bonds: B:S.226, B:G.228, B:G.228, B:G.228
Water bridges: B:D.204

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Chobanian, H.R. et al., Improved Stability of Proline-Derived Direct Thrombin Inhibitors through Hydroxyl to Heterocycle Replacement. Acs Med.Chem.Lett. (2015)

Release Date

2015-06-17

Peptides

Thrombin light chain: A
Thrombin heavy chain: B
Hirudin: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
H

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

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