Crystal structure of pteridine reductase 1 (PTR1) from trypanosoma brucei in ternary complex with cofactor (NADP+) and inhibitor 2-amino-5-(2-phenylethyl)-3,7-dihydro-4H- PYRROLO[2,3-D]PYRIMIDIN-4-one (DX6)

Structure

x-ray diffraction · 2 distinct chains · 47% helix, 14% strand (DSSP).

Ligands and binding sites

• NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
• DX6 · 2-amino-5-(2-phenylethyl)-3,7-dihydro-4H-pyrrolo[2,3-d]pyrimidin-4-one · ligand · 3 copies · chains A, B, C
• DTT · 2,3-dihydroxy-1,4-dithiobutane · additive · chains D

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

Pockets

7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Interfaces

6 interfaces between chains.

• B–D · 1888 Ų buried · 12 hydrogen bonds · protein-protein
• A–C · 1831 Ų buried · 9 hydrogen bonds · protein-protein
• A–B · 1427 Ų buried · 9 hydrogen bonds · protein-protein
• C–D · 1405 Ų buried · 11 hydrogen bonds · protein-protein
• A–D · 565 Ų buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 modified (oxidation).

Compared structures

• 3JQB · Crystal structure of pteridine reductase 1 (PTR1) from Trypanosoma brucei in ternary… · the same entry in another collection · chain B against B, TM-score 1.00

Analyse

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• Elsewhere: RCSB PDB 3JQB · PDBe 3JQB · UniProt Q581W1