6VRU

PIM-inhibitor complex 1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.179 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report

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This is version 1.2 of the entry. See complete history


Literature

Discovery of SARxxxx92, a pan-PIM kinase inhibitor, efficacious in a KG1 tumor model.

Barberis, C.Erdman, P.Czekaj, M.Fire, L.Pribish, J.Tserlin, E.Maniar, S.Batchelor, J.D.Liu, J.Patel, V.F.Hebert, A.Levit, M.Wang, A.Sun, F.Huang, S.A.

(2020) Bioorg Med Chem Lett 30: 127625-127625

  • DOI: https://doi.org/10.1016/j.bmcl.2020.127625
  • Primary Citation of Related Structures:  
    6VRU, 6VRV

  • PubMed Abstract: 

    N-substituted azaindoles were discovered as potent pan-PIM inhibitors. Lead optimization, guided by structure and focused on physico-chemical properties allowed us to solve inherent hERG and permeability liabilities, and provided compound 27, which subsequently impacted KG-1 tumor growth in a mouse model.


  • Organizational Affiliation

    IDD Medicinal Chemistry, Sanofi, 153 Second Avenue, Waltham MA 02451, United States. 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
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ROY (Subject of Investigation/LOI)
Query on ROY

Download Ideal Coordinates CCD File 
C [auth A]3,4-dichloro-2-cyclopropyl-1-[(piperidin-4-yl)methyl]-1H-pyrrolo[2,3-b]pyridine-6-carboxamide
C17 H20 Cl2 N4 O
LYLJXIKZRAZYFB-UHFFFAOYSA-N
IMD
Query on IMD

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

Download Ideal Coordinates CCD File 
D [auth A]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.179 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.555α = 90
b = 98.555β = 90
c = 81.009γ = 120
Software Package:
Software NamePurpose
CNSrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
SCALEPACKdata scaling
CNXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-11-04
    Type: Initial release
  • Version 1.1: 2020-11-25
    Changes: Database references
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Refinement description