Thrombin in complex with selective macrocyclic inhibitor

Structure

x-ray diffraction · 2 distinct chains · 18% helix, 31% strand (DSSP).

Ligands and binding sites

• T76 · (6r,21as)-17-chloro-6-cyclohexyl-2,3,6,7,10,11,19,20-octahydro-1H,5H-pyrrolo[1,2-k][1,4,8,11,14]benzoxatetraaza-cycloheptadecine-5,8,12,21(9h,13h,21ah)-tetrone · 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–H · 680 Ų buried · 9 hydrogen bonds · protein-protein

Modifications

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

Compared structures

• 1NT1 · thrombin in complex with selective macrocyclic 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 H against A, TM-score 0.52

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 1NT1 · PDBe 1NT1 · UniProt P00734 · UniProt P28504