7K6M | pdb_00007k6m

Crystal structure of PI3Kalpha selective Inhibitor PF-06843195

• PDB DOI: https://doi.org/10.2210/pdb7K6M/pdb

• Classification: SIGNALING PROTEIN, Transferase
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2020-09-21 Released: 2021-01-06 
• Deposition Author(s): Chen, P., Brooun, A., Deng, Y.L., Grodsky, N., Kaiser, S.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.41 Å
• R-Value Free: 
  0.232 (Depositor), 0.242 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.202 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Starting Model: other

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

• PubMed: 33356246 
• DOI: https://doi.org/10.1021/acs.jmedchem.0c01652
• Primary Citation 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 .

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Organizational Affiliation: 
• La Jolla Laboratories, Pfizer Worldwide Research and Development, 10770 Science Center Drive, San Diego, California 92121, United States.
Wuxi AppTec, 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, China.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 110.48 kDa 
• Atom Count: 7,204 
• Modeled Residue Count: 878 
• Deposited Residue Count: 946 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform	A	946	Homo sapiens	Mutation(s): 0  Gene Names: PIK3CA EC: 2.7.1.153 (PDB Primary Data), 2.7.11.1 (PDB Primary Data), 2.7.1.137 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P42336 (Homo sapiens) Explore P42336  Go to UniProtKB:  P42336
PHAROS:  P42336 GTEx:  ENSG00000121879

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
VXY (Subject of Investigation/LOI)	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 RTOREZYNLPQUKM-FQEVSTJZSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.41 Å
• R-Value Free:  0.232 (Depositor), 0.242 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.202 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.038	α = 90
b = 133.532	β = 90
c = 148.324	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-01-06 
Deposition Author(s): Chen, P., Brooun, A., Deng, Y.L., Grodsky, N., Kaiser, S.E.

Revision History  

• 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