8TS9

Human PI3K p85alpha/p110alpha H1047R bound to compound 1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.83 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.231 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Discovery and Clinical Proof-of-Concept of RLY-2608, a First-in-Class Mutant-Selective Allosteric PI3K alpha Inhibitor That Decouples Antitumor Activity from Hyperinsulinemia.

Varkaris, A.Pazolli, E.Gunaydin, H.Wang, Q.Pierce, L.Boezio, A.A.Bulku, A.DiPietro, L.Fridrich, C.Frost, A.Giordanetto, F.Hamilton, E.P.Harris, K.Holliday, M.Hunter, T.L.Iskandar, A.Ji, Y.Larivee, A.LaRochelle, J.R.Lescarbeau, A.Llambi, F.Lormil, B.Mader, M.M.Mar, B.G.Martin, I.McLean, T.H.Michelsen, K.Pechersky, Y.Puente-Poushnejad, E.Raynor, K.Rogala, D.Samadani, R.Schram, A.M.Shortsleeves, K.Swaminathan, S.Tajmir, S.Tan, G.Tang, Y.Valverde, R.Wehrenberg, B.Wilbur, J.Williams, B.R.Zeng, H.Zhang, H.Walters, W.P.Wolf, B.B.Shaw, D.E.Bergstrom, D.A.Watters, J.Fraser, J.S.Fortin, P.D.Kipp, D.R.

(2024) Cancer Discov 14: 240-257

  • DOI: https://doi.org/10.1158/2159-8290.CD-23-0944
  • Primary Citation of Related Structures:  
    8TS7, 8TS8, 8TS9, 8TSA, 8TSB, 8TSC, 8TSD, 8TU6

  • PubMed Abstract: 

    PIK3CA (PI3Kα) is a lipid kinase commonly mutated in cancer, including ∼40% of hormone receptor-positive breast cancer. The most frequently observed mutants occur in the kinase and helical domains. Orthosteric PI3Kα inhibitors suffer from poor selectivity leading to undesirable side effects, most prominently hyperglycemia due to inhibition of wild-type (WT) PI3Kα. Here, we used molecular dynamics simulations and cryo-electron microscopy to identify an allosteric network that provides an explanation for how mutations favor PI3Kα activation. A DNA-encoded library screen leveraging electron microscopy-optimized constructs, differential enrichment, and an orthosteric-blocking compound led to the identification of RLY-2608, a first-in-class allosteric mutant-selective inhibitor of PI3Kα. RLY-2608 inhibited tumor growth in PIK3CA-mutant xenograft models with minimal impact on insulin, a marker of dysregulated glucose homeostasis. RLY-2608 elicited objective tumor responses in two patients diagnosed with advanced hormone receptor-positive breast cancer with kinase or helical domain PIK3CA mutations, with no observed WT PI3Kα-related toxicities. Treatments for PIK3CA-mutant cancers are limited by toxicities associated with the inhibition of WT PI3Kα. Molecular dynamics, cryo-electron microscopy, and DNA-encoded libraries were used to develop RLY-2608, a first-in-class inhibitor that demonstrates mutant selectivity in patients. This marks the advance of clinical mutant-selective inhibition that overcomes limitations of orthosteric PI3Kα inhibitors. See related commentary by Gong and Vanhaesebroeck, p. 204 . See related article by Varkaris et al., p. 227 . This article is featured in Selected Articles from This Issue, p. 201.


  • Organizational Affiliation

    Mass General Cancer Center and Department of Medicine, Harvard Medical School, Boston, Massachusetts.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform1,060Homo sapiensMutation(s): 1 
Gene Names: PIK3CA
EC: 2.7.1.137 (UniProt), 2.7.11.1 (UniProt), 2.7.1.153 (UniProt)
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
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphatidylinositol 3-kinase regulatory subunit alpha300Homo sapiensMutation(s): 0 
Gene Names: PIK3R1
UniProt & NIH Common Fund Data Resources
Find proteins for P27986 (Homo sapiens)
Explore P27986 
Go to UniProtKB:  P27986
PHAROS:  P27986
GTEx:  ENSG00000145675 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP27986
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
UE9 (Subject of Investigation/LOI)
Query on UE9

Download Ideal Coordinates CCD File 
C [auth A]5-[3-fluoro-5-(trifluoromethyl)benzamido]-N-methyl-6-(2-methylanilino)pyridine-3-carboxamide
C22 H18 F4 N4 O2
ZQUWDKRQMSZGSZ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.83 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.231 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.24α = 90
b = 120.469β = 90
c = 191.338γ = 90
Software Package:
Software NamePurpose
ISOLDEmodel building
PHENIXrefinement
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-11-22
    Type: Initial release
  • Version 1.1: 2024-02-21
    Changes: Database references