Leishmania mexicana glyceraldehyde-3-phosphate dehydrogenase in complex with inhibitors

Structure

x-ray diffraction · 1 distinct chain · 30% helix, 26% strand (DSSP).

Ligands and binding sites

• TND · N-1,2,3,4-tetrahydronaphth-1-yl-2'-[3,5-dimethoxybenzamido]-2'-deoxy-adenosine · ligand · 6 copies · chains A, B, C, D, E, F

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

Pockets

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

Interfaces

7 interfaces between chains.

• A–D · 2128 Ų buried · 26 hydrogen bonds · protein-protein
• B–C · 2103 Ų buried · 25 hydrogen bonds · protein-protein
• E–F · 1441 Ų buried · 27 hydrogen bonds · protein-protein
• C–D · 1405 Ų buried · 18 hydrogen bonds · protein-protein
• A–B · 1403 Ų buried · 20 hydrogen bonds · protein-protein

Compared structures

• 1I33 · Leishmania mexicana glyceraldehyde-3-phosphate dehydrogenase in complex with inhibitors · the same entry in another collection · chain F against F, TM-score 1.00
• Q27890 · AlphaFold monomer V2.0 prediction for glyceraldehyde-3-phosphate dehydrogenase… · a predicted model of the same protein · chain B 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 Q27890
• Elsewhere: RCSB PDB 1I33 · PDBe 1I33 · UniProt Q27890