Leishmania major pteridine reductase 1 (PTR1) in complex with compound 3

Structure

x-ray diffraction · 4 distinct chains · 47% helix, 16% strand (DSSP).

Ligands and binding sites

• 6J6 · (2~{R})-2-[3,4-bis(oxidanyl)phenyl]-6-oxidanyl-2,3-dihydrochromen-4-one · ligand · 4 copies · chains A, D, B, C
• NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
• GOL · Glycerol · additive · 6 copies · chains A, C, B, D
• EDO · 1,2-ethanediol · additive · 5 copies · chains A, C, D
• ACT · Acetate ion · additive · 4 copies · chains A, B, D
• PGE · Triethylene glycol · additive · chains A, C

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

Pockets

13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Interfaces

6 interfaces between chains.

• A–B · 1748 Ų buried · 11 hydrogen bonds · protein-protein
• C–D · 1714 Ų buried · 10 hydrogen bonds · protein-protein
• A–C · 1617 Ų buried · 10 hydrogen bonds · protein-protein
• B–D · 1595 Ų buried · 8 hydrogen bonds · protein-protein
• B–C · 650 Ų buried · 13 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 modified (oxidation).

Compared structures

• 5L42 · Leishmania major Pteridine reductase 1 (PTR1) in complex with compound 3 · the same entry in another collection · chain D against D, TM-score 1.00
• Q01782 · AlphaFold monomer V2.0 prediction for pteridine reductase 1 (Q01782) · a predicted model of the same protein · chain A 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 Q01782
• Elsewhere: RCSB PDB 5L42 · PDBe 5L42 · UniProt Q01782