RCSB PDB - 4G11: X-ray structure of PI3K-gamma bound to a 4-(morpholin-4-yl)- (6-oxo-1,6-dihydropyrimidin-2-yl)amide inhibitor

 4G11

X-ray structure of PI3K-gamma bound to a 4-(morpholin-4-yl)- (6-oxo-1,6-dihydropyrimidin-2-yl)amide inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.349 
  • R-Value Work: 0.282 
  • R-Value Observed: 0.285 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

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This is version 1.1 of the entry. See complete history


Literature

Preparation and optimization of new 4-(morpholin-4-yl)-(6-oxo-1,6-dihydropyrimidin-2-yl)amide derivatives as PI3K beta inhibitors

Certal, V.Halley, F.Virone-Oddos, A.Thompson, F.Filoche-Romme, B.El-Ahmad, Y.Carry, J.C.Delorme, C.Karlsson, A.Abecassis, P.Y.Vincent, L.Bonnevaux, H.Nicolas, J.P.Morales, R.Michot, N.Vade, I.Louboutin, A.Perron, S.Doerflinger, G.Tric, B.Monget, S.Lengauer, C.Schio, L.

(2012) Bioorg Med Chem Lett 22: 6381-6384

  • DOI: https://doi.org/10.1016/j.bmcl.2012.08.072
  • Primary Citation of Related Structures:  
    4G11

  • PubMed Abstract: 

    From a HTS campaign, a new series of pyrimidone anilides exemplified by compound 1 has been identified with good inhibitory activity for the PI3Kβ isoform. The structure of compound 1 in PI3Kγ was solved revealing a binding mode in agreement with the SAR observed on PI3Kβ. These compounds displayed inhibition in the nanomolar range in the biochemical assay and were also potent p-Akt inhibitors in a PTEN-deficient PC3 prostate cancer cell line. Optimization of in vitro pharmocokinetic properties led to compound 25 exhibiting 52% bioavailability in mice and target engagement in an acute PK/PD study.


  • Organizational Affiliation

    Medicinal Chemistry Oncology Drug Discovery, Sanofi, Vitry-sur-Seine, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform966Homo sapiensMutation(s): 0 
Gene Names: PIK3CG
EC: 2.7.1.153 (PDB Primary Data), 2.7.11.1 (PDB Primary Data), 2.7.1.137 (UniProt), 2.7.1.154 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P48736 (Homo sapiens)
Explore P48736 
Go to UniProtKB:  P48736
PHAROS:  P48736
GTEx:  ENSG00000105851 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP48736
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
0W7
Query on 0W7

Download Ideal Coordinates CCD File 
B [auth A]2-[4-(morpholin-4-yl)-6-oxo-1,6-dihydropyrimidin-2-yl]-N-phenylacetamide
C16 H18 N4 O3
FPFCFOIMTFHSNY-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
0W7 BindingDB:  4G11 IC50: 1.00e+4 (nM) from 1 assay(s)
PDBBind:  4G11 IC50: 1.00e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.349 
  • R-Value Work: 0.282 
  • R-Value Observed: 0.285 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 140.63α = 90
b = 67.38β = 96.14
c = 105.89γ = 90
Software Package:
Software NamePurpose
DNAdata collection
MOLREPphasing
REFMACrefinement
PROCESSdata reduction
SCALAdata scaling

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 0W7Click on this verticalbar to view details

Entry History 

Deposition Data

  • Released Date: 2012-11-14 
  • Deposition Author(s): Morales, R.

Revision History  (Full details and data files)

  • Version 1.0: 2012-11-14
    Type: Initial release
  • Version 1.1: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description