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 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 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: 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 ...

    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. jpastor@cnio.es



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTO-ONCOGENE SERINE/THREONINE-PROTEIN KINASE PIM-1A308Homo sapiensMutation(s): 0 
Gene Names: PIM1
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
E46 (Subject of Investigation/LOI)
Query on E46

Download Ideal Coordinates CCD File 
B [auth A]N-(piperidin-4-ylmethyl)-3-[3-(trifluoromethyloxy)phenyl]-[1,2,3]triazolo[4,5-b]pyridin-5-amine
C18 H19 F3 N6 O
OZAALIWIRMBCOR-UHFFFAOYSA-N
 Ligand Interaction
IMD
Query on IMD

Download Ideal Coordinates CCD File 
C [auth A]IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
 Ligand Interaction
ACT
Query on ACT

Download Ideal Coordinates CCD File 
D [auth A]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
AL-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)
Binding MOAD:  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

View Full Validation Report



Ligand Structure Quality Assessment  



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