Crystal structue of thrombin in complex with a potent P1 heterocycle- aryl based inhibitor

Structure

x-ray diffraction · 2 distinct chains · 18% helix, 30% strand (DSSP).

Ligands and binding sites

• 170 · (2-[6-chloro-3-{[2,2-difluoro-2-(1-oxidopyridin-2-yl)ethyl]amino}-2-oxopyrazin-1(2H)-yl]-N-[5-chloro-2-(1H-tetrazol-1-yl)benzyl]acetamide · ligand · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 686 Ų buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide, 1 modified (disulfide, sulfation).

Compared structures

• 1SL3 · crystal structue of Thrombin in complex with a potent P1 heterocycle-Aryl based inhibitor · the same entry in another collection · chain A against A, TM-score 1.00
• P28504 · AlphaFold monomer V2.0 prediction for hirudin-2 (P28504) · a predicted model of the same protein · chain B against A, TM-score 0.55

Analyse

• Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
• Every structure of UniProt P00734
• Every structure of UniProt P28504
• Elsewhere: RCSB PDB 1SL3 · PDBe 1SL3 · UniProt P00734 · UniProt P28504