5SXC

Crystal Structure of PI3Kalpha in complex with fragment 8


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.55 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Identification of allosteric binding sites for PI3K alpha oncogenic mutant specific inhibitor design.

Miller, M.S.Maheshwari, S.McRobb, F.M.Kinzler, K.W.Amzel, L.M.Vogelstein, B.Gabelli, S.B.

(2017) Bioorg Med Chem 25: 1481-1486

  • DOI: 10.1016/j.bmc.2017.01.012
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • PIK3CA, the gene that encodes the catalytic subunit of phosphatidylinositol 3-kinase α (PI3Kα), is frequently mutated in breast and other types of cancer. A specific inhibitor that targets the mutant forms of PI3Kα could maximize treatment efficiency ...

    PIK3CA, the gene that encodes the catalytic subunit of phosphatidylinositol 3-kinase α (PI3Kα), is frequently mutated in breast and other types of cancer. A specific inhibitor that targets the mutant forms of PI3Kα could maximize treatment efficiency while minimizing side-effects. Herein we describe the identification of novel binding pockets that may provide an opportunity for the design of mutant selective inhibitors. Using a fragment-based approach, we screened a library of 352 fragments (MW<300Da) for binding to PI3Kα by X-ray crystallography. Five novel binding pockets were identified, each providing potential opportunities for inhibitor design. Of particular interest was a binding pocket near Glu542, which is located in one of the two most frequently mutated domains.


    Organizational Affiliation

    Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, United States; Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, United States; Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, United States. Electronic address: gabelli@jhmi.edu.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform
A
1096Homo sapiensMutation(s): 0 
Gene Names: PIK3CA
EC: 2.7.1.153 (PDB Primary Data), 2.7.11.1 (PDB Primary Data)
Find proteins for P42336 (Homo sapiens)
Go to UniProtKB:  P42336
NIH Common Fund Data Resources
PHAROS  P42336
Protein Feature View
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Phosphatidylinositol 3-kinase regulatory subunit alpha
B
279Homo sapiensMutation(s): 0 
Gene Names: PIK3R1GRB1
Find proteins for P27986 (Homo sapiens)
Go to UniProtKB:  P27986
NIH Common Fund Data Resources
PHAROS  P27986
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
URF
Query on URF

Download CCD File 
A
5-FLUOROURACIL
C4 H3 F N2 O2
GHASVSINZRGABV-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
AL-PEPTIDE LINKINGC3 H8 N O6 PSER
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.55 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.197 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 114.735α = 90
b = 117.271β = 90
c = 150.299γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
REFMACphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesCA062924 and CA043460
Alexander and Margaret Stewart TrustUnited States--

Revision History 

  • Version 1.0: 2017-02-15
    Type: Initial release
  • Version 1.1: 2017-09-20
    Changes: Author supporting evidence
  • Version 1.2: 2019-12-04
    Changes: Author supporting evidence