Geometry of binding of the benzamidine-and arginine-based inhibitors N-alpha-(2-naphthyl-sulphonyl-glycyl)-dl-P-amidinophenylalanyl- piperidine (napap) and (2R,4R)-4-methyl-1-[N-alpha-(3-methyl-1,2,3,4- tetrahydro-8-quinolinesulphonyl)-L-arginyl]-2-piperidine carboxylic acid (mqpa) to human alpha-thrombin: X-ray crystallographic determination of the napap-trypsin complex and modeling of napap- thrombin and mqpa-thrombin

Structure

x-ray diffraction · 1 distinct chain · 10% helix, 34% strand (DSSP).

Ligands and binding sites

• MID · 1-[N-(naphthalen-2-ylsulfonyl)glycyl-4-carbamimidoyl-D-phenylalanyl]piperidine · ligand · chains E
• CA · Calcium ion · metal · chains E

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

• 1PPC · Geometry of binding of the benzamidine-and arginine-based inhibitors… · the same entry in another collection · chain E against E, TM-score 1.00
• 1TNH · Prediction of novel serine protease inhibitors · a predicted model of the same protein · chain E against A, TM-score 1.00
• 1TNG · Prediction of novel serine protease inhibitors · a predicted model of the same protein · chain E against A, TM-score 1.00
• 1TNK · Prediction of novel serine protease inhibitors · a predicted model of the same protein · chain E against A, TM-score 1.00
• 1TNL · Prediction of novel serine protease inhibitors · a predicted model of the same protein · chain E against A, TM-score 1.00
• 1TNJ · Prediction of novel serine protease inhibitors · a predicted model of the same protein · chain E against A, TM-score 1.00
• 1TNI · Prediction of novel serine protease inhibitors · a predicted model of the same protein · chain E against A, TM-score 1.00
• P00760 · AlphaFold monomer V2.0 prediction for cationic trypsin (P00760) · a predicted model of the same protein · chain E against A, TM-score 1.00

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 P00760
• Elsewhere: RCSB PDB 1PPC · PDBe 1PPC · UniProt P00760