GDP-bound KRAS G12D in complex with TH-Z835

Structure

x-ray diffraction · resolution 1.99 · 1 distinct chain · 37% helix, 25% strand (DSSP).

Ligands and binding sites

• 05I · 4-[(1~{S},5~{R})-3,8-diazabicyclo[3.2.1]octan-3-yl]-7-(8-methylnaphthalen-1-yl)-2-[[(2~{S})-1-methylpyrrolidin-2-yl]methoxy]-6,8-dihydro-5~{H}-pyrido[3,4-d]pyrimidine · ligand · 3 copies · chains A, B, C
• GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · 2 copies · chains B, C
• GDP · Guanosine-5'-diphosphate · ligand · chains A
• MG · Magnesium ion · metal · 3 copies · chains A, B, C

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

Pockets

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

Interfaces

3 interfaces between chains.

• A–B · 611 Ų buried · 15 hydrogen bonds · protein-protein
• B–C · 376 Ų buried · 5 hydrogen bonds · protein-protein
• A–C · 363 Ų buried · 4 hydrogen bonds · protein-protein

Compared structures

• 7EWB · GDP-bound KRAS G12D in complex with th-Z835 · the same entry in another collection · 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 P01116
• Elsewhere: RCSB PDB 7EWB · PDBe 7EWB · UniProt P01116