7K71

Crystal structure of PI3Kalpha inhibitor 4-0686


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.244 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure-Based Drug Design and Synthesis of PI3K alpha-Selective Inhibitor (PF-06843195).

Cheng, H.Orr, S.T.M.Bailey, S.Brooun, A.Chen, P.Deal, J.G.Deng, Y.L.Edwards, M.P.Gallego, G.M.Grodsky, N.Huang, B.Jalaie, M.Kaiser, S.Kania, R.S.Kephart, S.E.Lafontaine, J.Ornelas, M.A.Pairish, M.Planken, S.Shen, H.Sutton, S.Zehnder, L.Almaden, C.D.Bagrodia, S.Falk, M.D.Gukasyan, H.J.Ho, C.Kang, X.Kosa, R.E.Liu, L.Spilker, M.E.Timofeevski, S.Visswanathan, R.Wang, Z.Meng, F.Ren, S.Shao, L.Xu, F.Kath, J.C.

(2021) J Med Chem 64: 644-661

  • DOI: 10.1021/acs.jmedchem.0c01652
  • Primary Citation of Related Structures:  
    7K6M, 7K71, 7K6N, 7K6O

  • PubMed Abstract: 
  • The phosphoinositide 3-kinase (PI3K)/mammalian target of rapamycin (mTOR) signaling pathway is a frequently dysregulated pathway in human cancer, and PI3Kα is one of the most frequently mutated kinases in human cancer. A PI3Kα-selective inhibitor may provide the opportunity to spare patients the side effects associated with broader inhibition of the class I PI3K family ...

    The phosphoinositide 3-kinase (PI3K)/mammalian target of rapamycin (mTOR) signaling pathway is a frequently dysregulated pathway in human cancer, and PI3Kα is one of the most frequently mutated kinases in human cancer. A PI3Kα-selective inhibitor may provide the opportunity to spare patients the side effects associated with broader inhibition of the class I PI3K family. Here, we describe our efforts to discover a PI3Kα-selective inhibitor by applying structure-based drug design (SBDD) and computational analysis. A novel series of compounds, exemplified by 2,2-difluoroethyl (3 S )-3-{[2'-amino-5-fluoro-2-(morpholin-4-yl)-4,5'-bipyrimidin-6-yl]amino}-3-(hydroxymethyl)pyrrolidine-1-carboxylate ( 1) (PF-06843195), with high PI3Kα potency and unique PI3K isoform and mTOR selectivity were discovered. We describe here the details of the design and synthesis program that lead to the discovery of 1 .


    Organizational Affiliation

    La Jolla Laboratories, Pfizer Worldwide Research and Development, 10770 Science Center Drive, San Diego, California 92121, United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoformA946Homo sapiensMutation(s): 0 
Gene Names: PIK3CA
EC: 2.7.1.153 (PDB Primary Data), 2.7.11.1 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P42336 (Homo sapiens)
Explore P42336 
Go to UniProtKB:  P42336
PHAROS:  P42336
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
VYP
Query on VYP

Download Ideal Coordinates CCD File 
B [auth A]2-(morpholin-4-yl)[4,5'-bipyrimidin]-2'-amine
C12 H14 N6 O
WCSNDONKXWSCEI-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.244 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.68α = 90
b = 135.28β = 90
c = 142.17γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-01-06
    Type: Initial release
  • Version 1.1: 2021-01-27
    Changes: Database references