SMTL ID : 6zuh.1

Crystal Structure of Thrombin in complex with compound17

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x N6H: [2-[(3-chlorophenyl)methylamino]-7-methoxy-1,3-benzoxazol-5-yl]-(2,2-dimethylmorpholin-4-yl)methanone(Non-covalent)

N6H.1: 20 residues within 4Å: Chain B: H.43, Y.47, W.50, E.94, N.95, L.96, I.179, D.199, A.200, C.201, E.202, S.205, V.225, S.226, W.227, G.228, G.230, G.238, F.239, Y.240 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:W.50, B:V.225, B:W.227, B:W.227 Hydrogen bonds: B:S.205, B:G.228 Water bridges: B:S.205 Halogen bonds: B:F.239

1 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.2: 1 residues within 4Å: Chain B: N.53 No protein-ligand interaction detected (PLIP)

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

DMS.3: 3 residues within 4Å: Chain B: S.176, G.235, K.236 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hillisch, A. et al., Design, Synthesis, and Pharmacological Characterization of a Neutral, Non-Prodrug Thrombin Inhibitor with Good Oral Pharmacokinetics. J.Med.Chem. (2020)

Release Date

2020-08-26

Peptides

Prothrombin: A
Prothrombin: B
Hirudin-2: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
L

B
H

C
I

Prothrombin

Prothrombin

Hirudin-2

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