Thrombin in complex with selective macrocyclic inhibitor at 1.8A

Structure

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

Ligands and binding sites

• L86 · (11S)-11-benzyl-6-chloro-1,2,10,11,12,13,14,15,16,17,18,19-dodecahydro-5,9-methano-2,5,8,10,13,17-benzohexaazacycloheni cosine-3,24-dione · 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 · 695 Ų buried · 6 hydrogen bonds · protein-protein

Modifications

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

Compared structures

• 1NM6 · thrombin in complex with selective macrocyclic inhibitor at 1.8A · 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 1NM6 · PDBe 1NM6 · UniProt P00734 · UniProt P28504