› 4bcg

X-ray diffraction
3.08Å resolution

Structure of CDK9 in complex with cyclin T and a 2-amino-4-heteroaryl- pyrimidine inhibitor

Released:
DOI: 10.2210/pdb4bcg/pdb
PDB entry 4bcg coloured by chain, front view.
PDB entry 4bcg coloured by chain, side view.
PDB entry 4bcg coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Substituted 4-(thiazol-5-yl)-2-(phenylamino)pyrimidines are highly active CDK9 inhibitors: synthesis, X-ray crystal structures, structure-activity relationship, and anticancer activities.
Shao H, Shi S, Huang S, Hole AJ, Abbas AY, Baumli S, Liu X, Lam F, Foley DW, Fischer PM, Noble M, Endicott JA, Pepper C, Wang S
J Med Chem 56 640-59 (2013)
PMID: 23301767

Function and Biology Details

Reactions catalysed: 
ATP + a protein = ADP + a phosphoprotein
ATP + [DNA-directed RNA polymerase] = ADP + [DNA-directed RNA polymerase] phosphate
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-130021 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Cyclin-dependent kinase 9 Chain: A
Molecule details ›
Chain: A
Length: 331 amino acids
Theoretical weight: 38.05 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: P50750 (Residues: 2-330; Coverage: 88%)
Gene names: CDC2L4, CDK9, TAK
Sequence domains: Protein kinase domain
Structure domains:
Cyclin-T1 Chain: B
Molecule details ›
Chain: B
Length: 260 amino acids
Theoretical weight: 30.12 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: O60563 (Residues: 2-259; Coverage: 36%)
Gene name: CCNT1
Sequence domains:
Structure domains: Cyclin-like

Ligands and Environments

2 bound ligands:
Ligand T3C 1 x T3C
Ligand GOL 2 x GOL
1 modified residue:
Ligand TPO 1 x TPO

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I03
Spacegroup: R3
Unit cell:
a: 172.8Å b: 172.8Å c: 98.88Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.163 0.161 0.197
Expression system: Spodoptera frugiperda

Quick links

Citations

8 review citations

Targeting cyclin-dependent kinases in anti-neoplastic therapy.
Bruyère et al. (2013)
7 more

9 mentions without citation

Structure-based discovery of cyclin-dependent protein kinase inhibitors.
Martin et al. (2017)
8 more