Crystal structures of a high-affinity macrocyclic peptide mimetic in complex with the GRB2 SH2 domain

Structure

x-ray diffraction · 2 distinct chains · 16% helix, 25% strand (DSSP).

Ligands and binding sites

• S1S · 2-(4-((9S,10S,14S,Z)-18-(2-amino-2-oxoethyl)-9-(carboxymethyl)-14-(naphthalen-1-ylmethyl)-8,17,20-trioxo-7,16,19-triazaspiro[5.14]icos-11-en-10-yl)phenyl)malonic acid · ligand · 3 copies · chains A, B
• P33 · 3,6,9,12,15,18-hexaoxaicosane-1,20-diol · additive · chains A, B

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

Pockets

2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 1970 Ų buried · 15 hydrogen bonds · protein-protein

Compared structures

• 2AOA · Crystal structures of a high-affinity macrocyclic peptide mimetic in complex with the… · the same entry in another collection · chain A against A, TM-score 1.00
• P62993 · AlphaFold monomer V2.0 prediction for growth factor receptor-bound protein 2 (P62993) · a predicted model of the same protein · chain A against A, TM-score 0.68

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 P62993
• Elsewhere: RCSB PDB 2AOA · PDBe 2AOA · UniProt P62993