Crystal structure of MKK7 (MAP2K7) in complex with ibrutnib, with covalent and allosteric binding modes

Structure

x-ray diffraction · resolution 2 · 1 distinct chain · 41% helix, 18% strand (DSSP).

Ligands and binding sites

• 1E8 · 1-{(3R)-3-[4-amino-3-(4-phenoxyphenyl)-1H-pyrazolo[3,4-d]pyrimidin-1-yl]piperidin-1-yl}prop-2-en-1-one · ligand · chains A
• 8E8 · 1-[(3~{R})-3-[4-azanyl-3-(4-phenoxyphenyl)pyrazolo[3,4-d]pyrimidin-1-yl]piperidin-1-yl]propan-1-one · ligand · chains A
• EDO · 1,2-ethanediol · additive · 8 copies · chains A
• DMS · Dimethyl sulfoxide · additive · 4 copies · chains A

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

Pockets

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

Modifications

Observed in the structure: 1 covalent (covalent ligand).

Compared structures

• 6YG2 · Crystal structure of MKK7 (MAP2K7) in complex with ibrutnib, with covalent and allosteric… · the same entry in another collection · chain A against A, TM-score 1.00
• O14733 · AlphaFold monomer V2.0 prediction for dual specificity mitogen- activated protein kinase… · a predicted model of the same protein · chain A against A, TM-score 0.86

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 O14733
• Elsewhere: RCSB PDB 6YG2 · PDBe 6YG2 · UniProt O14733