Crystal structure of thrombin in complex with inhibitor 15

Structure

x-ray diffraction · 2 distinct chains · 17% helix, 30% strand (DSSP).

Ligands and binding sites

• T15 · 2-{3-[(benzylsulfonyl)amino]-6-methyl-2-oxopyridin-1(2H)-yl}-N-({1-[2-(tert-butylamino)-2-oxoethyl]-4-methyl-1H-imidazol-5-yl}methyl)acetamide · ligand · chains A

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

Pockets

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

Interfaces

1 interface between chains.

• A–B · 690 Ų buried · 10 hydrogen bonds · protein-protein

Modifications

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

Compared structures

• 3C1K · Crystal structure of thrombin in complex with inhibitor 15 · the same entry in another collection · chain A against A, TM-score 1.00
• P28511 · AlphaFold monomer V2.0 prediction for hirudin-3B' (P28511) · a predicted model of the same protein · chain B against A, TM-score 0.46

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 P28511
• Elsewhere: RCSB PDB 3C1K · PDBe 3C1K · UniProt P00734 · UniProt P28511