5TEX

Pim-1 kinase in complex with a 7-azaindole


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.184 

wwPDB Validation 3D Report Full Report



Literature

Discovery of N-substituted 7-azaindoles as PIM1 kinase inhibitors - Part I.

Barberis, C.Moorcroft, N.Arendt, C.Levit, M.Moreno-Mazza, S.Batchelor, J.Mechin, I.Majid, T.

(2017) Bioorg Med Chem Lett 27: 4730-4734

  • DOI: 10.1016/j.bmcl.2017.08.069
  • Primary Citation of Related Structures:  
    5KCX, 5TEX, 5TEL, 5TOE, 5TUR

  • PubMed Abstract: 
  • Novel N-substituted azaindoles have been discovered as PIM1 inhibitors. X-ray structures have played a significant role in orienting the chemistry effort in the initial phase of hit confirmation. Disclosure of an unconventional binding mode for 1 and ...

    Novel N-substituted azaindoles have been discovered as PIM1 inhibitors. X-ray structures have played a significant role in orienting the chemistry effort in the initial phase of hit confirmation. Disclosure of an unconventional binding mode for 1 and 2, as demonstrated by X-ray crystallography, is presented and was an important factor in selecting and advancing a lead series.


    Organizational Affiliation

    IDD Medicinal Chemistry, Sanofi Genzyme, 153 Second Avenue, Waltham MA 02451, USA; Program Management, Sanofi Genzyme, 49 New York Avenue, Framingham MA 01701, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Serine/threonine-protein kinase pim-1A274Homo sapiensMutation(s): 0 
Gene Names: PIM1
EC: 2.7.11.1
Find proteins for P11309 (Homo sapiens)
Explore P11309 
Go to UniProtKB:  P11309
NIH Common Fund Data Resources
PHAROS  P11309
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
7AU
Query on 7AU

Download CCD File 
A
(4-{4-chloro-1-methyl-2-[4-(piperazin-1-yl)phenyl]-1H-pyrrolo[2,3-b]pyridin-3-yl}phenyl)methanol
C25 H25 Cl N4 O
LGVBWTYRZTXNEO-UHFFFAOYSA-N
 Ligand Interaction
IMD
Query on IMD

Download CCD File 
A
IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
7AUIC50:  400   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.184 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.536α = 90
b = 97.536β = 90
c = 81.104γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-10-11
    Type: Initial release