PQR530 [(S)-4-(Difluoromethyl)-5-(4-(3-methylmorpholino)-6-morpholino-1,3,5-triazin-2-yl)pyridin-2-amine] bound to the PI3Ka catalytic subunit p110alpha

Experimental Data Snapshot

  • Resolution: 3.15 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.245 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.4 of the entry. See complete history


(S)-4-(Difluoromethyl)-5-(4-(3-methylmorpholino)-6-morpholino-1,3,5-triazin-2-yl)pyridin-2-amine (PQR530), a Potent, Orally Bioavailable, and Brain-Penetrable Dual Inhibitor of Class I PI3K and mTOR Kinase.

Rageot, D.Bohnacker, T.Keles, E.McPhail, J.A.Hoffmann, R.M.Melone, A.Borsari, C.Sriramaratnam, R.Sele, A.M.Beaufils, F.Hebeisen, P.Fabbro, D.Hillmann, P.Burke, J.E.Wymann, M.P.

(2019) J Med Chem 62: 6241-6261

  • DOI: https://doi.org/10.1021/acs.jmedchem.9b00525
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The phosphoinositide 3-kinase (PI3K)/mechanistic target of rapamycin (mTOR) pathway is frequently overactivated in cancer, and drives cell growth, proliferation, survival, and metastasis. Here, we report a structure-activity relationship study, which led to the discovery of a drug-like adenosine 5'-triphosphate-site PI3K/mTOR kinase inhibitor: ( S )-4-(difluoromethyl)-5-(4-(3-methylmorpholino)-6-morpholino-1,3,5-triazin-2-yl)pyridin-2-amine (PQR530, compound 6 ), which qualifies as a clinical candidate due to its potency and specificity for PI3K and mTOR kinases, and its pharmacokinetic properties, including brain penetration. Compound 6 showed excellent selectivity over a wide panel of kinases and an excellent selectivity against unrelated receptor enzymes and ion channels. Moreover, compound 6 prevented cell growth in a cancer cell line panel. The preclinical in vivo characterization of compound 6 in an OVCAR-3 xenograft model demonstrated good oral bioavailability, excellent brain penetration, and efficacy. Initial toxicity studies in rats and dogs qualify 6 for further development as a therapeutic agent in oncology.

  • Organizational Affiliation

    Department of Biomedicine , University of Basel , Mattenstrasse 28 , 4058 Basel , Switzerland.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform948Homo sapiensMutation(s): 0 
Gene Names: PIK3CA
EC: (PDB Primary Data), (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P42336 (Homo sapiens)
Explore P42336 
Go to UniProtKB:  P42336
PHAROS:  P42336
GTEx:  ENSG00000121879 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP42336
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
M1J (Subject of Investigation/LOI)
Query on M1J

Download Ideal Coordinates CCD File 
B [auth A]4-(difluoromethyl)-5-{4-[(3S)-3-methylmorpholin-4-yl]-6-(morpholin-4-yl)-1,3,5-triazin-2-yl}pyridin-2-amine
C18 H23 F2 N7 O2
Experimental Data & Validation

Experimental Data

  • Resolution: 3.15 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.245 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.926α = 90
b = 135.511β = 90
c = 144.498γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Canadian Institutes of Health Research (CIHR)Canada142393

Revision History  (Full details and data files)

  • Version 1.0: 2019-06-26
    Type: Initial release
  • Version 1.1: 2019-07-10
    Changes: Data collection, Database references
  • Version 1.2: 2019-07-24
    Changes: Data collection, Database references
  • Version 1.3: 2020-01-08
    Changes: Author supporting evidence
  • Version 1.4: 2023-10-11
    Changes: Data collection, Database references, Refinement description