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SMTL ID : 2c8y.1

thrombin inhibitors

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

DMS.1:	3 residues within 4Å: Chain B: E.124, T.125, S.128 1 PLIP interactions: 1 interactions with chain B pi-Cation interactions: B:F.215
DMS.2:	5 residues within 4Å: Chain B: L.130, A.132, I.167, R.170, F.186 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.132
DMS.4:	7 residues within 4Å: Chain B: C.28, H.43, E.202, G.203, D.204, S.205 Ligands: C3M.5 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.203

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

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:Y.190, B:D.234

1 x C3M: N-[(2R,3S)-3-AMINO-2-HYDROXY-4-PHENYLBUTYL]NAPHTHALENE-2-SULFONAMIDE(Non-covalent)

C3M.5:

12 residues within 4Å:

Chain B: H.43, Y.47, W.50, E.94, N.95, L.96, S.205, S.226, W.227, G.228, E.229
Ligands: DMS.4

13 PLIP interactions:

13 interactions with chain B

Hydrophobic interactions: B:W.50, B:L.96, B:L.96, B:W.227, B:W.227
Hydrogen bonds: B:S.205, B:S.205, B:G.228
Water bridges: B:G.230, B:G.230, B:G.230
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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