› 3vc4

X-ray diffraction
2.23Å resolution

Exploitation of hydrogen bonding constraints and flat hydrophobic energy landscapes in Pim-1 kinase needle screening and inhibitor design

Released:
DOI: 10.2210/pdb3vc4/pdb
PDB entry 3vc4 coloured by chain, front view.
PDB entry 3vc4 coloured by chain, side view.
PDB entry 3vc4 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Implications of promiscuous Pim-1 kinase fragment inhibitor hydrophobic interactions for fragment-based drug design.
Good AC, Liu J, Hirth B, Asmussen G, Xiang Y, Biemann HP, Bishop KA, Fremgen T, Fitzgerald M, Gladysheva T, Jain A, Jancsics K, Metz M, Papoulis A, Skerlj R, Stepp JD, Wei RR
J Med Chem 55 2641-8 (2012)
PMID: 22339127

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: 34.48 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
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 IMD 2 x IMD
Ligand 0FS 1 x 0FS
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 5.0.3
Spacegroup: P65
Unit cell:
a: 98.496Å b: 98.496Å c: 81.025Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.319 0.257 0.319
Expression system: Escherichia coli

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Citations

4 review citations

Finding novel pharmaceuticals in the systems biology era using multiple effective drug targets, phenotypic screening and knowledge of transporters: where drug discovery went wrong and how to fix it.
Kell DB. (2013)
3 more

2 mentions without citation

Identification of the first inhibitor of the GBP1:PIM1 interaction. Implications for the development of a new class of anticancer agents against paclitaxel resistant cancer cells.
Andreoli et al. (2014)
1 more