› 5lmk

X-ray diffraction
2.4Å resolution

Structure of phopsho-CDK2-cyclin A in complex with an ATP-competitive inhibitor

Released:
DOI: 10.2210/pdb5lmk/pdb
PDB entry 5lmk coloured by chain, front view.
PDB entry 5lmk coloured by chain, side view.
PDB entry 5lmk coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Explicit treatment of active-site waters enhances quantum mechanical/implicit solvent scoring: Inhibition of CDK2 by new pyrazolo[1,5-a]pyrimidines.
Hylsová M, Carbain B, Fanfrlík J, Musilová L, Haldar S, Köprülüoğlu C, Ajani H, Brahmkshatriya PS, Jorda R, Kryštof V, Hobza P, Echalier A, Paruch K, Lepšík M
Eur J Med Chem 126 1118-1128 (2017)
PMID: 28039837

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-148886 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Cyclin-dependent kinase 2 Chain: A
Molecule details ›
Chain: A
Length: 299 amino acids
Theoretical weight: 34.14 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: 258 amino acids
Theoretical weight: 29.62 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P20248 (Residues: 175-432; Coverage: 60%)
Gene names: CCN1, CCNA, CCNA2
Sequence domains:
Structure domains: Cyclin-like
Cyclin-dependent kinase 2 Chain: C
Molecule details ›
Chain: C
Length: 297 amino acids
Theoretical weight: 33.87 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P24941 (Residues: 1-296; Coverage: 99%)
Gene names: CDK2, CDKN2
Sequence domains: Protein kinase domain
Structure domains:

Ligands and Environments

3 bound ligands:
Ligand 6ZK 2 x 6ZK
Ligand SGM 2 x SGM
Ligand MG 1 x MG
1 modified residue:
Ligand TPO 2 x TPO

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-1
Spacegroup: P212121
Unit cell:
a: 74.466Å b: 134.395Å c: 149.481Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.213 0.212 0.249
Expression system: Escherichia coli

Quick links

Citations

3 review citations

Functional Pyrazolo[1,5-a]pyrimidines: Current Approaches in Synthetic Transformations and Uses As an Antitumor Scaffold.
Arias-Gómez et al. (2021)
2 more