Crystal structure of B-RAF kinase domain in complex with a DIHYDROPYRIDO[2,3-D]PYRIMIDINONE-based inhibitor

Structure

x-ray diffraction · 2 distinct chains · 38% helix, 13% strand (DSSP).

Ligands and binding sites

• T1Q · N-(2,4-difluoro-3-{2-[(3-hydroxypropyl)amino]-8-methyl-7-oxo-7,8-dihydropyrido[2,3-d]pyrimidin-6-yl}phenyl)propane-1-sulfonamide · ligand · 2 copies · chains A, B

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 · 1197 Ų buried · 17 hydrogen bonds · protein-protein

Compared structures

• 4E4X · Crystal Structure of B-Raf Kinase Domain in Complex with a Dihydropyrido[2,3-d]pyrimidi… · the same entry in another collection · chain A against A, TM-score 1.00
• P15056 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein kinase B-RAF (P15056) · a predicted model of the same protein · chain A against A, TM-score 0.97

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 P15056
• Elsewhere: RCSB PDB 4E4X · PDBe 4E4X · UniProt P15056