› 3dcv

X-ray diffraction
2.7Å resolution

Crystal structure of human Pim1 kinase complexed with 4-(4-hydroxy-3-methyl-phenyl)-6-phenylpyrimidin-2(1H)-one

Released:
DOI: 10.2210/pdb3dcv/pdb
PDB entry 3dcv coloured by chain, front view.
PDB entry 3dcv coloured by chain, side view.
PDB entry 3dcv coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
4-(1H-indazol-5-yl)-6-phenylpyrimidin-2(1H)-one analogs as potent CDC7 inhibitors.
Shafer CM, Lindvall M, Bellamacina C, Gesner TG, Yabannavar A, Jia W, Lin S, Walter A
Bioorg Med Chem Lett 18 4482-5 (2008)
PMID: 18672368

Function and Biology Details

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

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-145753 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Serine/threonine-protein kinase pim-1 Chain: A
Molecule details ›
Chain: A
Length: 328 amino acids
Theoretical weight: 37.6 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: P11309 (Residues: 2-313; Coverage: 100%)
Gene name: PIM1
Sequence domains: Protein kinase domain
Structure domains:

Ligands and Environments

1 bound ligand:
Ligand 55E 1 x 55E
1 modified residue:
Ligand SEP 1 x SEP

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL9-2
Spacegroup: P65
Unit cell:
a: 97.59Å b: 97.59Å c: 81.258Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.182 0.179 0.234
Expression system: Escherichia coli BL21

Quick links

Citations

3 review citations

Cdc7 kinase - a new target for drug development.
Swords et al. (2010)
2 more

6 mentions without citation

The Development of CK2 Inhibitors: From Traditional Pharmacology to in Silico Rational Drug Design.
Cozza G. (2017)
5 more