› 5v80

X-ray diffraction
2.25Å resolution

PIM1 kinase in complex with Cpd1 (1-methyl-4-(3-(6-(piperazin-1-yl)pyridin-2-yl)-1H-pyrazolo[3,4-c]pyridin-5-yl)piperazin-2-one)

Released:
DOI: 10.2210/pdb5v80/pdb
PDB entry 5v80 coloured by chain, front view.
PDB entry 5v80 coloured by chain, side view.
PDB entry 5v80 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Discovery of 5-Azaindazole (GNE-955) as a Potent Pan-Pim Inhibitor with Optimized Bioavailability.
Wang X, Kolesnikov A, Tay S, Chan G, Chao Q, Do S, Drummond J, Ebens AJ, Liu N, Ly J, Harstad E, Hu H, Moffat J, Munugalavadla V, Murray J, Slaga D, Tsui V, Volgraf M, Wallweber H, Chang JH
J Med Chem 60 4458-4473 (2017)
PMID: 28445037

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: 299 amino acids
Theoretical weight: 34.45 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P11309 (Residues: 29-313; Coverage: 91%)
Gene name: PIM1
Sequence domains: Protein kinase domain
Structure domains:

Ligands and Environments

2 bound ligands:
Ligand PO4 1 x PO4
Ligand 971 1 x 971
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 5.0.2
Spacegroup: P65
Unit cell:
a: 97.669Å b: 97.669Å c: 80.579Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.177 0.175 0.212
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

2 review citations

Recent Advances in Indazole-Containing Derivatives: Synthesis and Biological Perspectives.
Zhang et al. (2018)
1 more

1 mention without citation

Chemical space exploration based on recurrent neural networks: applications in discovering kinase inhibitors.
Li et al. (2020)