4A7C

Crystal structure of PIM1 kinase with ETP46546

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.171 

Starting Model: experimental
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This is version 1.4 of the entry. See complete history. 


Literature

Hit to Lead Evaluation of 1,2,3-Triazolo[4,5-B]Pyridines as Pim Kinase Inhibitors.

Pastor, J., Oyarzabal, J., Saluste, G., Alvarez, R.M., Rivero, V., Ramos, F., Cendon, E., Blanco-Aparicio, C., Ajenjo, N., Cebria, A., Albarran, M.I., Cebrian, D., Corrionero, A., Fominaya, J., Montoya, G., Mazzorana, M.

(2012) Bioorg Med Chem Lett 22: 1591

  • DOI: https://doi.org/10.1016/j.bmcl.2011.12.130
  • Primary Citation of Related Structures:  
    4A7C

  • PubMed Abstract: 

    PIM kinases have become targets of interest due to their association with biochemical mechanisms affecting survival, proliferation and cytokine production. 1,2,3-Triazolo[4,5-b]pyridines were identified as PIM inhibitors applying a scaffold hopping approach. Initial exploration around this scaffold and X-ray crystallographic data are hereby described.

    • Organizational Affiliation: 

    Experimental Therapeutics Program, Spanish National Cancer Research Centre (CNIO), Madrid, Spain. [email protected]


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PROTO-ONCOGENE SERINE/THREONINE-PROTEIN KINASE PIM-1308Homo sapiensMutation(s): 0 
EC: 2.7.1.37 (PDB Primary Data), 2.7.11.1 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P11309 (Homo sapiens)
Explore P11309 
Go to UniProtKB:  P11309
PHAROS:  P11309
GTEx:  ENSG00000137193 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11309
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
SEP
Query on SEP
A
L-PEPTIDE LINKINGC3 H8 N O6 PSER
Binding Affinity Annotations 
IDSourceBinding Affinity
E46 BindingDB:  4A7C IC50: 6 (nM) from 1 assay(s)
EC50: 45 (nM) from 1 assay(s)
PDBBind:  4A7C IC50: 6 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.171 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.355α = 90
b = 99.355β = 90
c = 81.119γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-02-15
    Type: Initial release
  • Version 1.1: 2012-05-23
    Changes: Other
  • Version 1.2: 2015-01-14
    Changes: Non-polymer description
  • Version 1.3: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description
  • Version 1.4: 2024-11-13
    Changes: Structure summary