DFRA1 complexed with NADPH and 5-(3-(7-(4-(AMINOMETHYL)PHENYL) BENZO[D][1,3]DIOXOL-5-YL)BUT-1-yn-1-yl)-6-ethylpyrimidine-2,4-diamine (UCP1223)

Structure

x-ray diffraction · 2 distinct chains · 23% helix, 36% strand (DSSP).

Ligands and binding sites

• NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
• 8MU · 5-[(3S)-3-{7-[4-(aminomethyl)phenyl]-2H-1,3-benzodioxol-5-yl}but-1-yn-1-yl]-6-ethylpyrimidine-2,4-diamine · ligand · 2 copies · chains A, B
• 560 · 5-[(3R)-3-{7-[4-(aminomethyl)phenyl]-2H-1,3-benzodioxol-5-yl}but-1-yn-1-yl]-6-ethylpyrimidine-2,4-diamine · ligand · chains B
• CA · Calcium ion · metal · 2 copies · chains A, B

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

Pockets

2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 976 Ų buried · 10 hydrogen bonds · protein-protein

Compared structures

• 7RGJ · DfrA1 complexed with NADPH and 5-(3-(7-(4-(aminomethyl)phenyl)benzo[d][1,3]dioxol-5-yl)but… · the same entry in another collection · chain A against A, TM-score 1.00
• P00382 · AlphaFold monomer V2.0 prediction for dihydrofolate reductase type 1 (P00382) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 P00382
• Elsewhere: RCSB PDB 7RGJ · PDBe 7RGJ · UniProt P00382