Crystal structure of an active KRAS G12D (gppcp) dimer in complex with bi-5747

Structure

x-ray diffraction · 2 distinct chains · 38% helix, 27% strand (DSSP).

Ligands and binding sites

• GCP · Phosphomethylphosphonic acid guanylate ester · ligand · 4 copies · chains A, B, C, D
• R6W · (3~{S})-5-oxidanyl-3-[2-[[6-[[3-[(1~{S})-6-oxidanyl-3-oxidanylidene-1,2-dihydroisoindol-1-yl]-1~{H}-indol-2-yl]methylamino]hexylamino]methyl]-1~{H}-indol-3-yl]-2, 3-dihydroisoindol-1-one · ligand · 2 copies · chains A, C, D, B
• MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
• EDO · 1,2-ethanediol · additive · chains A, C

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

Pockets

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

Interfaces

5 interfaces between chains.

• A–D · 531 Ų buried · 7 hydrogen bonds · protein-protein
• B–C · 512 Ų buried · 6 hydrogen bonds · protein-protein
• B–D · 199 Ų buried · 5 hydrogen bonds · protein-protein
• A–C · 196 Ų buried · 4 hydrogen bonds · protein-protein
• C–D · 176 Ų buried · 0 hydrogen bonds · protein-protein

Compared structures

• 7ACA · Crystal structure of an active KRAS G12D (gppcp) dimer in complex with bi-5747 · 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 7ACA · PDBe 7ACA · UniProt P01116