› 3umw

X-ray diffraction
2.08Å resolution

Crystal structure of Pim1 kinase in complex with inhibitor (Z)-2-[(1H-indazol-3-yl)methylene]-6-methoxy-7-(piperazin-1-ylmethyl)benzofuran-3(2H)-one

Released:
DOI: 10.2210/pdb3umw/pdb
PDB entry 3umw coloured by chain, front view.
PDB entry 3umw coloured by chain, side view.
PDB entry 3umw coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Rational evolution of a novel type of potent and selective proviral integration site in Moloney murine leukemia virus kinase 1 (PIM1) inhibitor from a screening-hit compound.
Nakano H, Saito N, Parker L, Tada Y, Abe M, Tsuganezawa K, Yokoyama S, Tanaka A, Kojima H, Okabe T, Nagano T
J Med Chem 55 5151-64 (2012)
PMID: 22540945

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:
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: 298 amino acids
Theoretical weight: 34.19 KDa
Source organism: Homo sapiens
Expression system: cell-free protein synthesis
UniProt:
  • Canonical: P11309 (Residues: 29-313; Coverage: 91%)
Gene name: PIM1
Sequence domains: Protein kinase domain
Structure domains:

Ligands and Environments

3 bound ligands:
Ligand GOL 1 x GOL
Ligand SO4 1 x SO4
Ligand 596 1 x 596
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL26B2
Spacegroup: P65
Unit cell:
a: 98.28Å b: 98.28Å c: 80.641Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.175 0.174 0.2
Expression system: cell-free protein synthesis

Quick links

Citations

6 review citations

The PIM family of serine/threonine kinases in cancer.
Narlik-Grassow et al. (2014)
5 more

6 mentions without citation

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