Human thrombin complexed with novel synthetic peptide mimetic inhibitor and hirugen

Structure

x-ray diffraction · 3 distinct chains · 16% helix, 31% strand (DSSP).

Ligands and binding sites

• 0ZE · [[[(4S,5S)-4-[[(3S,6S,8aR)-6-azanyl-5-oxo-6-(phenylmethyl)-1,2,3,7,8,8a-hexahydroindolizin-3-yl]carbonylamino]-5-(1,3-b enzothiazol-2-yl)-5-hydroxy-pentyl]amino]-azanyl-methylidene]azanium · ligand · chains H
• NA · Sodium ion · metal · 2 copies · chains H

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

2 interfaces between chains.

• L–H · 1149 Ų buried · 25 hydrogen bonds · protein-protein
• H–I · 627 Ų buried · 7 hydrogen bonds · protein-protein

Modifications

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

Compared structures

• 1B5G · Human thrombin complexed with novel synthetic peptide mimetic inhibitor and hirugen · the same entry in another collection · chain L against L, TM-score 1.00
• P00734 · AlphaFold monomer V2.0 prediction for prothrombin (P00734) · a predicted model of the same protein · chain H against A, TM-score 0.92
• P09945 · AlphaFold monomer V2.0 prediction for hirudin variant-2 (P09945) · a predicted model of the same protein · chain I against A, TM-score 0.48

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 P09945
• Elsewhere: RCSB PDB 1B5G · PDBe 1B5G · UniProt P00734 · UniProt P09945