Design and discovery of novel, potent thrombin inhibitors with a solubilizing cationic P1-P2-linker

Structure

x-ray diffraction · 3 distinct chains · 13% helix, 30% strand (DSSP).

Ligands and binding sites

• 5CB · N-(5-chloro-benzo[b]thiophen-3-ylmethyl)-2-[6-chloro-oxo-3-(2-pyridin-2-yl-ethylamino)-2H-pyrazin-1-yl]-acetamide · 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

2 interfaces between chains.

• H–L · 1102 Ų buried · 24 hydrogen bonds · protein-protein
• H–I · 625 Ų buried · 6 hydrogen bonds · protein-protein

Modifications

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

Compared structures

• 2BVX · Design and Discovery of Novel, Potent Thrombin Inhibitors with a Solubilizing Cationic… · the same entry in another collection · chain L against L, TM-score 1.00
• P09945 · AlphaFold monomer V2.0 prediction for hirudin variant-2 (P09945) · a predicted model of the same protein · chain I against A, TM-score 0.52

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 P09945
• Elsewhere: RCSB PDB 2BVX · PDBe 2BVX · UniProt P00734 · UniProt P09945