› 6oql

X-ray diffraction
2.71Å resolution

CDK6 in complex with Cpd13 (R)-5-fluoro-4-(4-methyl-5,6,7,8-tetrahydro-4H-pyrazolo[1,5-a]azepin-3-yl)-N-(5-(4-methylpiperazin-1-yl)pyridin-2-yl)pyrimidin-2-amine

Released:
DOI: 10.2210/pdb6oql/pdb
PDB entry 6oql coloured by chain, front view.
PDB entry 6oql coloured by chain, side view.
PDB entry 6oql coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Design of a brain-penetrant CDK4/6 inhibitor for glioblastoma.
Bronner SM, Merrick KA, Murray J, Salphati L, Moffat JG, Pang J, Sneeringer CJ, Dompe N, Cyr P, Purkey H, Boenig GL, Li J, Kolesnikov A, Larouche-Gauthier R, Lai KW, Shen X, Aubert-Nicol S, Chen YC, Cheong J, Crawford JJ, Hafner M, Haghshenas P, Jakalian A, Leclerc JP, Lim NK, O'Brien T, Plise EG, Shalan H, Sturino C, Wai J, Xiao Y, Yin J, Zhao L, Gould S, Olivero A, Heffron TP
Bioorg Med Chem Lett 29 2294-2301 (2019)
PMID: 31307887

Function and Biology Details

Reaction catalysed: 
ATP + a protein = ADP + a phosphoprotein
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-169439 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Cyclin-dependent kinase 6 Chain: A
Molecule details ›
Chain: A
Length: 291 amino acids
Theoretical weight: 33.07 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: Q00534 (Residues: 11-301; Coverage: 89%)
Gene names: CDK6, CDKN6
Sequence domains: Protein kinase domain

Ligands and Environments

1 bound ligand:
Ligand N1A 1 x N1A
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL12-2
Spacegroup: I4
Unit cell:
a: 101.668Å b: 101.668Å c: 60.113Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.206 0.204 0.253
Expression system: Spodoptera frugiperda

Quick links

Citations

8 review citations

Glioma: molecular signature and crossroads with tumor microenvironment.
Barthel et al. (2022)
7 more

1 mention without citation

Identification of abemaciclib derivatives targeting cyclin-dependent kinase 4 and 6 using molecular dynamics, binding free energy calculation, synthesis, and pharmacological evaluation.
Zhou et al. (2023)