Crystal structure of KRAS-G12D in complex with natural product-like compound 15

Structure

x-ray diffraction · 1 distinct chain · 40% helix, 26% strand (DSSP).

Ligands and binding sites

• GCP · Phosphomethylphosphonic acid guanylate ester · ligand · 2 copies · chains A, B
• JJN · (6~{a}~{R},11~{b}~{S})-6~{a}-(1,4-dimethylpiperidin-4-yl)-7,11~{b}-dihydro-6~{H}-indolo[2,3-c]isoquinolin-5-one · ligand · chains A, B
• MG · Magnesium ion · metal · 2 copies · chains A, B
• EDO · 1,2-ethanediol · additive · 2 copies · chains B, A

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

Pockets

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

Interfaces

1 interface between chains.

• A–B · 739 Ų buried · 10 hydrogen bonds · protein-protein

Compared structures

• 6QUX · Crystal Structure of KRAS-G12D in Complex with Natural Product-Like Compound 15 · 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 6QUX · PDBe 6QUX · UniProt P01116