Structure of CDK2 in complex with cyclin a and a 2-amino-4- heteroaryl-pyrimidine inhibitor

Structure

x-ray diffraction · 4 distinct chains · 50% helix, 9% strand (DSSP).

Ligands and binding sites

• T6Q · 2-[[3-(4-ethanoyl-1,4-diazepan-1-yl)phenyl]amino]-4-[4-methyl-2-(methylamino)-1,3-thiazol-5-yl]pyrimidine-5-carbonitrile · ligand · 2 copies · chains A, C
• SO4 · Sulfate ion · ion · 2 copies · chains B, C, A, D
• SGM · Monothioglycerol · additive · 4 copies · chains B, D

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

Pockets

13 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Interfaces

5 interfaces between chains.

• C–D · 1650 Ų buried · 26 hydrogen bonds · protein-protein
• A–B · 1577 Ų buried · 29 hydrogen bonds · protein-protein
• A–D · 467 Ų buried · 3 hydrogen bonds · protein-protein
• B–C · 439 Ų buried · 1 hydrogen bond · protein-protein
• A–C · 35 Ų buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 covalent, 2 modified (additive adduct, phosphorylation).

Compared structures

• 4BCO · Structure of CDK2 in complex with cyclin A and a 2-amino-4-heteroaryl- pyrimidine… · the same entry in another collection · chain D against D, TM-score 1.00
• P30274 · AlphaFold monomer V2.0 prediction for cyclin-A2 (P30274) · a predicted model of the same protein · chain D against A, TM-score 1.00
• 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 0.91

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 P30274
• Elsewhere: RCSB PDB 4BCO · PDBe 4BCO · UniProt P24941 · UniProt P30274