SMTL ID : 3bv9.1

Structure of Thrombin Bound to the Inhibitor FM19

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

hetero-1-1-mer

Ligands

1 x DAR- OIC- PRO- DAL- 4PH- NH2: FM19 inhibitor(Non-covalent)

DAR-OIC-PRO-DAL-4PH-NH2.1: 17 residues within 4Å: Chain B: H.43, Y.47, W.50, N.95, L.96, I.179, D.199, A.200, C.201, E.202, S.205, V.225, W.227, G.228, E.229, G.230, G.238 23 PLIP interactions: 23 interactions with chain B Hydrophobic interactions: B:Y.47, B:W.50, B:W.50, B:W.50, B:L.96, B:I.179, B:W.227, B:W.227 Hydrogen bonds: B:A.200, B:G.228, B:G.230 Water bridges: B:W.227, B:E.229, B:E.229, B:G.230, B:G.230, B:G.230, B:G.230, B:G.230, B:G.230, B:D.232, B:Y.240 Salt bridges: B:D.199

3 x IOD: IODIDE ION(Non-functional Binders)

IOD.2: 5 residues within 4Å: Chain B: H.87, R.245, L.246, W.249 Ligands: GOL.6 Ligand excluded by PLIP IOD.3: 2 residues within 4Å: Chain B: M.80, K.107 Ligand excluded by PLIP IOD.4: 2 residues within 4Å: Chain B: R.170, F.186 Ligand excluded by PLIP

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

NA.5: 3 residues within 4Å: Chain B: Y.190, R.233, K.236 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Y.190, B:K.236 Water bridges: B:Y.190, B:R.197, B:G.238

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 6 residues within 4Å: Chain B: H.87, P.88, R.89, K.248, W.249 Ligands: IOD.2 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.252, B:K.252 GOL.7: 2 residues within 4Å: Chain B: P.48, N.53 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nieman, M.T. et al., Thrombostatin FM compounds: direct thrombin inhibitors - mechanism of action in vitro and in vivo. J.Thromb.Haemost. (2008)

Release Date

2008-03-04

Peptides

Thrombin light chain: A
Thrombin heavy chain: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Thrombin light chain

Thrombin heavy chain

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