5KCX

Pim-1 kinase in Complex with a Selective N-substituted 7-azaindole Inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.190 

wwPDB Validation 3D Report Full Report


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: 10.1016/j.bmcl.2017.08.069
  • Primary Citation of Related Structures:  

  • 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.,IDD Medicinal Chemistry, Sanofi Genzyme, 153 Second Avenue, Waltham MA 02451, USA; Program Management, Sanofi Genzyme, 49 New York Avenue, Framingham MA 01701, USA.,IDD Medicinal Chemistry, Sanofi Genzyme, 153 Second Avenue, Waltham MA 02451, USA. Electronic address: claude.barberis2@sanofi.com.,Oncology Biochemistry/Biology, Sanofi Genzyme, 270 Albany Street, Cambridge, MA 02139, USA.,IDD In Vitro Biology, Sanofi, 153 Second Avenue, Waltham MA 02451, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Serine/threonine-protein kinase pim-1
A
291Homo sapiensMutation(s): 0 
Gene Names: PIM1
EC: 2.7.11.1
Find proteins for P11309 (Homo sapiens)
Go to Gene View: PIM1
Go to UniProtKB:  P11309
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
6S3
Query on 6S3

Download SDF File 
Download CCD File 
A
4-chloranyl-1-methyl-2-[4-(4-methylpiperazin-1-yl)phenyl]pyrrolo[2,3-b]pyridine-6-carboxamide
C20 H22 Cl N5 O
ZHUIPHDJCHSZFK-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

Download SDF File 
Download CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
IMD
Query on IMD

Download SDF File 
Download CCD File 
A
IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.190 
  • Space Group: P 65
Unit Cell:
Length (Å)Angle (°)
a = 98.010α = 90.00
b = 98.010β = 90.00
c = 80.670γ = 120.00
Software Package:
Software NamePurpose
CNXrefinement
CNXphasing
HKL-2000data scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-07-19
    Type: Initial release
  • Version 1.1: 2017-10-18
    Type: Database references