SMTL ID : 2pks.1

Thrombin in complex with inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

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

NA.1: 2 residues within 4Å: Chain C: R.79, K.82 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.79, C:K.82

1 x G44: 4-({[4-(3-METHYLBENZOYL)PYRIDIN-2-YL]AMINO}METHYL)BENZENECARBOXIMIDAMIDE(Non-covalent)

G44.2: 15 residues within 4Å: Chain B: H.43, W.50, E.94, L.96 Chain C: I.25, D.45, A.46, C.47, E.48, S.51, S.72, W.73, G.74, G.76, G.84 12 PLIP interactions: 1 interactions with chain B, 11 interactions with chain C Hydrogen bonds: B:H.43, C:D.45, C:A.46, C:S.51 Hydrophobic interactions: C:I.25, C:A.46, C:W.73, C:W.73 Water bridges: C:D.45, C:S.51, C:F.85, C:Y.86

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Blomberg, D. et al., Design, synthesis and biological evaluation of thrombin inhibitors based on a pyridine scaffold. Org.Biomol.Chem. (2007)

Release Date

2008-04-22

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Thrombin light chain

Thrombin heavy chain fragment

Thrombin heavy chain fragment

Hirudin

Related Entries With Identical Sequence