Refined 2.3 ångströms X-ray crystal structure of bovine thrombin complexes formed with the benzamidine and arginine-based thrombin inhibitors napap, 4-tapap and mqpa: a starting point for improving antithrombotics

Structure

x-ray diffraction · 2 distinct chains · 14% helix, 31% strand (DSSP).

Ligands and binding sites

• MIT · amino{[(4S)-5-[(2R,4R)-2-carboxy-4-methylpiperidin-1-yl]-4-({[(3R)-3-methyl-1,2,3,4-tetrahydroquinolin-8-yl]sulfonyl}amino)-5-oxopentyl]amino}methaniminium · ligand · 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

1 interface between chains.

• L–H · 1429 Ų buried · 30 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

• 1ETR · Refined 2.3 ångströms X-ray crystal structure of bovine thrombin complexes formed with… · the same entry in another collection · chain L against L, TM-score 1.00
• P00735 · AlphaFold monomer V2.0 prediction for prothrombin (P00735) · a predicted model of the same protein · chain H against A, TM-score 0.96

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 P00735
• Elsewhere: RCSB PDB 1ETR · PDBe 1ETR · UniProt P00735