› 3cy2

X-ray diffraction
2.01Å resolution

Crystal structure of human proto-oncogene serine threonine kinase (PIM1) in complex with a consensus peptide and a beta carboline ligand II

Released:
DOI: 10.2210/pdb3cy2/pdb
PDB entry 3cy2 coloured by chain, front view.
PDB entry 3cy2 coloured by chain, side view.
PDB entry 3cy2 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
7,8-dichloro-1-oxo-β-carbolines as a versatile scaffold for the development of potent and selective kinase inhibitors with unusual binding modes.
Huber K, Brault L, Fedorov O, Gasser C, Filippakopoulos P, Bullock AN, Fabbro D, Trappe J, Schwaller J, Knapp S, Bracher F
J Med Chem 55 403-13 (2012)
PMID: 22136433

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-145758 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Serine/threonine-protein kinase pim-1 Chain: A
Molecule details ›
Chain: A
Length: 314 amino acids
Theoretical weight: 35.72 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P11309 (Residues: 1-313; Coverage: 100%)
Gene name: PIM1
Sequence domains: Protein kinase domain
Structure domains:
Pimtide peptide Chain: B
Molecule details ›
Chain: B
Length: 14 amino acids
Theoretical weight: 1.59 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

3 bound ligands:
Ligand CL 1 x CL
Ligand MB9 1 x MB9
Ligand EDO 1 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU FR-E+ SUPERBRIGHT
Spacegroup: P65
Unit cell:
a: 98.668Å b: 98.668Å c: 81.129Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.169 0.167 0.199
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

2 review citations

Death-associated protein kinase (DAPK) family modulators: Current and future therapeutic outcomes.
Farag et al. (2019)
1 more

6 mentions without citation

Binding of protein kinase inhibitors to synapsin I inferred from pair-wise binding site similarity measurements.
Defranchi et al. (2010)
5 more