5SWO

Crystal Structure of PI3Kalpha in complex with fragments 4 and 19


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.5 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.1 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
  • Primary Citation of Related Structures:  

  • 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.,Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, United States.,Schrödinger, Inc., 120 West 45th Street, New York, NY 10036, United States.,Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, United States.,Ludwig Center and Howard Hughes Medical Institutions, Johns Hopkins University School of Medicine, Baltimore, MD 21287, United States.




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
Find proteins for P42336 (Homo sapiens)
Go to Gene View: PIK3CA
Go to UniProtKB:  P42336
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Phosphatidylinositol 3-kinase regulatory subunit alpha
B
279Homo sapiensMutation(s): 0 
Gene Names: PIK3R1 (GRB1)
Find proteins for P27986 (Homo sapiens)
Go to Gene View: PIK3R1
Go to UniProtKB:  P27986
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
2ZV
Query on 2ZV

Download SDF File 
Download CCD File 
B
4-methyl-3-nitropyridin-2-amine
C6 H7 N3 O2
IKMZGACFMXZAAT-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
70T
Query on 70T

Download SDF File 
Download CCD File 
A
2-methyl-5-nitro-1H-indole
C9 H8 N2 O2
IDJGRXQMAHESOD-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
A
L-PEPTIDE LINKINGC3 H8 N O6 PSER
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.5 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.189 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 114.826α = 90.00
b = 116.360β = 90.00
c = 149.442γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
REFMACphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data collection
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer InstituteUnited 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
    Type: Author supporting evidence