Crystal structure of PI3Kalpha selective Inhibitor PF-06843195

Experimental Data Snapshot

  • Resolution: 2.41 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.196 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.3 of the entry. See complete history


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

  • 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. 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform946Homo 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
VXY (Subject of Investigation/LOI)
Query on VXY

Download Ideal Coordinates CCD File 
B [auth A]2,2-difluoroethyl (3S)-3-{[2'-amino-5-fluoro-2-(morpholin-4-yl)[4,5'-bipyrimidin]-6-yl]amino}-3-(hydroxymethyl)pyrrolidine-1-carboxylate
C20 H25 F3 N8 O4
Experimental Data & Validation

Experimental Data

  • Resolution: 2.41 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.196 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.038α = 90
b = 133.532β = 90
c = 148.324γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

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
  • Version 1.2: 2024-03-06
    Changes: Data collection, Database references
  • Version 1.3: 2024-04-03
    Changes: Refinement description