› 8h6p

X-ray diffraction
2.44Å resolution

Complex structure of CDK2/Cyclin E1 and a potent, selective macrocyclic inhibitor

Released:
DOI: 10.2210/pdb8h6p/pdb
PDB entry 8h6p coloured by chain, front view.
PDB entry 8h6p coloured by chain, side view.
PDB entry 8h6p coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Accelerated Discovery of Macrocyclic CDK2 Inhibitor QR-6401 by Generative Models and Structure-Based Drug Design.
Yu Y, Huang J, He H, Han J, Ye G, Xu T, Sun X, Chen X, Ren X, Li C, Li H, Huang W, Liu Y, Wang X, Gao Y, Cheng N, Guo N, Chen X, Feng J, Hua Y, Liu C, Zhu G, Xie Z, Yao L, Zhong W, Chen X, Liu W, Li H
ACS Med Chem Lett 14 297-304 (2023)
PMID: 36923916

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-150301 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Cyclin-dependent kinase 2 Chain: A
Molecule details ›
Chain: A
Length: 298 amino acids
Theoretical weight: 34.04 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P24941 (Residues: 1-297; Coverage: 100%)
Gene names: CDK2, CDKN2
Sequence domains: Protein kinase domain
G1/S-specific cyclin-E1 Chain: B
Molecule details ›
Chain: B
Length: 271 amino acids
Theoretical weight: 31.66 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P24864 (Residues: 103-373; Coverage: 66%)
Gene names: CCNE, CCNE1
Sequence domains:

Ligands and Environments

1 bound ligand:
Ligand WZU 1 x WZU
1 modified residue:
Ligand TPO 1 x TPO

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL02U1
Spacegroup: P41212
Unit cell:
a: 101.588Å b: 101.588Å c: 152.425Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.222 0.221 0.292
Expression system: Escherichia coli

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