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SMTL ID : 2c93.1

thrombin inhibitors

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

DMS.1:	4 residues within 4Å: Chain B: E.124, T.125, S.128, F.215 1 PLIP interactions: 1 interactions with chain B pi-Cation interactions: B:F.215
DMS.3:	8 residues within 4Å: Chain B: L.27, C.28, H.43, E.202, G.203, D.204, S.205 Ligands: C4M.4 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.203 Water bridges: B:K.52 Salt bridges: B:E.202

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

NA.2:

2 residues within 4Å:

Chain B: R.233, K.236

5 PLIP interactions:

5 interactions with chain B

Hydrogen bonds: B:R.233, B:K.236
Water bridges: B:D.234, B:G.235, B:G.238

1 x C4M: N-[(2R,3S)-3-AMINO-2-HYDROXY-4-PHENYLBUTYL]-4-METHOXY-2,3,6-TRIMETHYLBENZENESULFONAMIDE(Non-covalent)

C4M.4:

14 residues within 4Å:

Chain B: H.43, Y.47, W.50, W.92, E.94, N.95, L.96, I.179, E.202, S.226, W.227, G.228, E.229
Ligands: DMS.3

15 PLIP interactions:

15 interactions with chain B

Hydrophobic interactions: B:H.43, B:W.50, B:W.50, B:L.96, B:I.179, B:W.227, B:W.227, B:E.229
Hydrogen bonds: B:E.202, B:G.228, B:G.228, B:G.228
Water bridges: B:E.202
pi-Stacking: B:H.43, B:Y.47

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Howard, N. et al., Application of Fragment Screening and Fragment Linking to the Discovery of Novel Thrombin Inhibitors. J.Med.Chem. (2006)

Release Date

2006-07-04

Peptides

THROMBIN, LIGHT CHAIN: A
THROMBIN HEAVY CHAIN: B
HIRUDIN VARIANT-2: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

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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