› 3f5x

X-ray diffraction
2.4Å resolution

CDK-2-Cyclin complex with indazole inhibitor 9 bound at its active site

Released:
DOI: 10.2210/pdb3f5x/pdb
PDB entry 3f5x coloured by chain, front view.
PDB entry 3f5x coloured by chain, side view.
PDB entry 3f5x coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
2-(6-Phenyl-1H-indazol-3-yl)-1H-benzo[d]imidazoles: design and synthesis of a potent and isoform selective PKC-zeta inhibitor.
Trujillo JI, Kiefer JR, Huang W, Thorarensen A, Xing L, Caspers NL, Day JE, Mathis KJ, Kretzmer KK, Reitz BA, Weinberg RA, Stegeman RA, Wrightstone A, Christine L, Compton R, Li X
Bioorg Med Chem Lett 19 908-11 (2009)
PMID: 19097791

Function and Biology Details

Reaction catalysed: 
ATP + a protein = ADP + a phosphoprotein
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assemblies composition:
hetero octamer
hetero tetramer
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-148886 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Cyclin-dependent kinase 2 Chains: A, C
Molecule details ›
Chains: A, C
Length: 298 amino acids
Theoretical weight: 33.98 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P24941 (Residues: 1-298; Coverage: 100%)
Gene names: CDK2, CDKN2
Sequence domains: Protein kinase domain
Structure domains:
Cyclin-A2 Chains: B, D
Molecule details ›
Chains: B, D
Length: 256 amino acids
Theoretical weight: 29.43 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: P20248 (Residues: 177-432; Coverage: 59%)
Gene names: CCN1, CCNA, CCNA2
Sequence domains:
Structure domains: Cyclin-like

Ligands and Environments

3 bound ligands:
Ligand GOL 2 x GOL
Ligand EZV 2 x EZV
Ligand SO4 1 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 17-ID
Spacegroup: P6222
Unit cell:
a: 184.051Å b: 184.051Å c: 214.848Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.266 0.266 0.283
Expression systems:
  • Escherichia coli
  • Spodoptera frugiperda

Quick links

Citations

5 review citations

Protein kinase C: perfectly balanced.
Newton AC. (2018)
4 more

2 mentions without citation

HOMCOS: an updated server to search and model complex 3D structures.
Kawabata T. (2016)
1 more