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SMTL ID : 1ca8.1

Thrombin inhibitors with rigid tripeptidyl aldehydes

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

NA.1:	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:R.197, B:G.238
NA.2:	2 residues within 4Å: Chain B: K.174, T.177 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.174

1 x 0KV: 2-{(3S)-3-[(benzylsulfonyl)amino]-2-oxopiperidin-1-yl}-N-{(2S)-1-[(3S)-1-carbamimidoylpiperidin-3-yl]-3-oxopropan-2-yl}acetamide(Covalent)

0KV.3:

17 residues within 4Å:

Chain B: H.43, Y.47, W.50, E.94, L.96, I.179, D.199, A.200, C.201, E.202, S.205, S.226, W.227, G.228, E.229, G.230, G.238

15 PLIP interactions:

15 interactions with chain B

Hydrophobic interactions: B:Y.47, B:W.50, B:I.179, B:W.227, B:W.227
Hydrogen bonds: B:S.226, B:G.228, B:G.228, B:E.229, B:G.230
Water bridges: B:D.199, B:G.203, B:W.227, B:Y.240
Salt bridges: B:D.199

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Krishnan, R. et al., Highly selective mechanism-based thrombin inhibitors: structures of thrombin and trypsin inhibited with rigid peptidyl aldehydes. Biochemistry (1998)

Release Date

1999-04-27

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

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

HIRUGEN

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