5TEX | pdb_00005tex

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 (Depositor), 0.220 (DCC) 
  • R-Value Work: 
    0.181 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 
    0.184 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 7AUClick on this verticalbar to view details

This is version 1.1 of the entry. See complete history


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: https://doi.org/10.1016/j.bmcl.2017.08.069
  • Primary Citation of Related Structures:  
    5KCX, 5TEL, 5TEX, 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 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. Electronic address: claude.barberis2@sanofi.com.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/threonine-protein kinase pim-1274Homo sapiensMutation(s): 0 
Gene Names: PIM1
EC: 2.7.11.1
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
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
7AU
Query on 7AU

Download Ideal Coordinates CCD File 
C [auth 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
IMD
Query on IMD

Download Ideal Coordinates CCD File 
B [auth A]IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
Binding Affinity Annotations 
IDSourceBinding Affinity
7AU BindingDB:  5TEX IC50: 400 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free:  0.217 (Depositor), 0.220 (DCC) 
  • R-Value Work:  0.181 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 0.184 (Depositor) 
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



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 7AUClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-10-11
    Type: Initial release
  • Version 1.1: 2024-03-06
    Changes: Data collection, Database references