CDK2/CYCLIN A2 in complex with open-ring 5-nitrosopyrimidine inhibitor LC436

Structure

x-ray diffraction · 2 distinct chains · 50% helix, 9% strand (DSSP).

Ligands and binding sites

• K4W · 4-[[[5-nitroso-2-[[(2~{R})-1-oxidanylbutan-2-yl]amino]-6-(propan-2-ylamino)pyrimidin-4-yl]amino]methyl]phenol · ligand · 2 copies · chains A, C
• NA · Sodium ion · metal · 4 copies · chains A, B, C, D
• GOL · Glycerol · additive · 4 copies · chains B, C, D

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

Pockets

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

Interfaces

3 interfaces between chains.

• C–D · 1649 Ų buried · 29 hydrogen bonds · protein-protein
• A–B · 1622 Ų buried · 25 hydrogen bonds · protein-protein
• B–D · 382 Ų buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 modified (phosphorylation).

Compared structures

• 6RIJ · CDK2/cyclin A2 in complex with open-ring 5-nitrosopyrimidine inhibitor LC436 · 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 D 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 C against A, TM-score 0.91

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 6RIJ · PDBe 6RIJ · UniProt P24941 · UniProt P20248