SMTL ID : 2cn0.1

Complex of Recombinant Human Thrombin with a Designed Inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x F25: 4-(1R,3AS,4R,8AS,8BR)-[1-DIFLUOROMETHYL-2-(4-FLUOROBENZYL)-3-OXODECAHYDROPYRROLO[3,4-A]PYRROLIZIN-4-YL]BENZAMIDINE(Non-covalent)

F25.1: 23 residues within 4Å: Chain A: H.43, Y.47, W.50, K.52, E.94, N.95, L.96, I.179, D.199, A.200, C.201, E.202, G.203, S.205, V.225, S.226, W.227, G.228, G.230, C.231, D.232, G.238, F.239 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:V.225, A:W.227, A:W.227 Hydrogen bonds: A:D.199, A:D.199, A:G.228 Water bridges: A:F.239 Halogen bonds: A:E.94

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

NA.2: 5 residues within 4Å: Chain A: D.232, R.233, D.234, G.235, K.236 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.236, A:K.236 Water bridges: A:R.197, A:G.235, A:G.238

1 x CA: CALCIUM ION(Non-covalent)

CA.3: 4 residues within 4Å: Chain A: K.174, D.175, T.177, R.178 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:K.174, A:T.177, H2O.9, H2O.10

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hoffmann-Roder, A. et al., Mapping the Fluorophilicity of a Hydrophobic Pocket: Synthesis and Biological Evaluation of Tricyclic Thrombin Inhibitors Directing Fluorinated Alkyl Groups Into the P Pocket. Chemmedchem (2006)

Release Date

2006-11-06

Peptides

PROTHROMBIN PRECURSOR: A
HIRUDIN IIA: B
PROTHROMBIN PRECURSOR: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
I

C
L

PROTHROMBIN PRECURSOR

HIRUDIN IIA

PROTHROMBIN PRECURSOR

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