Differential binding of inhibitors to active and inactive CDK2 provides insights for drug design

Structure

x-ray diffraction · 2 distinct chains · 47% helix, 9% strand (DSSP).

Ligands and binding sites

• MTW · Hydroxy(oxo)(3-{[(2Z)-4-[3-(1H-1,2,4-triazol-1-ylmethyl)phenyl]pyrimidin-2(5H)-ylidene]amino}phenyl)ammonium · ligand · 2 copies · chains A, C

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

Pockets

11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Interfaces

5 interfaces between chains.

• C–D · 1752 Ų buried · 19 hydrogen bonds · protein-protein
• A–B · 1687 Ų buried · 17 hydrogen bonds · protein-protein
• A–D · 454 Ų buried · 2 hydrogen bonds · protein-protein
• B–C · 454 Ų buried · 5 hydrogen bonds · protein-protein
• A–C · 131 Ų buried · 1 hydrogen bond · protein-protein

Compared structures

• 2C5X · Differential Binding Of Inhibitors To Active And Inactive Cdk2 Provides Insights For Drug… · the same entry in another collection · chain D against D, TM-score 1.00
• P20248 · AlphaFold monomer V2.0 prediction for cyclin-A2 (P20248) · a predicted model of the same protein · chain B against A, TM-score 0.99
• P24941 · AlphaFold monomer V2.0 prediction for cyclin-dependent kinase 2 (P24941) · a predicted model of the same protein · chain A against A, TM-score 0.92

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 P24941
• Every structure of UniProt P20248
• Elsewhere: RCSB PDB 2C5X · PDBe 2C5X · UniProt P24941 · UniProt P20248