Human dihydrofolate reductase complexed with NADPH and 2,4-diamino-5- ((7,8-dicarbaundecaboran-7-YL)METHYL)-6-methylpyrimidine, a novel boron containing, nonclassical antifolate

Structure

x-ray diffraction · 1 distinct chain · 20% helix, 33% strand (DSSP).

Ligands and binding sites

• NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
• 39B · (S)-2,4-diamino-5-((7,8-dicarbaundecaboran-7-yl) methyl)-6-methylpyrimidine · ligand · 2 copies · chains A, B
• 39E · (R)-2,4-diamino-5-((7,8-dicarbaundecaboran-7-yl) methyl)-6-methylpyrimidine · ligand · 2 copies · chains A, B
• GOL · Glycerol · additive · chains B

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

Pockets

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

Interfaces

1 interface between chains.

• A–B · 333 Ų buried · 3 hydrogen bonds · protein-protein

Compared structures

• 2C2T · Human Dihydrofolate Reductase Complexed With NADPH and… · the same entry in another collection · chain A against A, TM-score 1.00
• P00374 · AlphaFold monomer V2.0 prediction for dihydrofolate reductase (P00374) · 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 P00374
• Elsewhere: RCSB PDB 2C2T · PDBe 2C2T · UniProt P00374