Macromolecule Content

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

7K6M

Crystal structure of PI3Kalpha selective Inhibitor PF-06843195

PDB DOI: 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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
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 1.1 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

PubMed: 33356246 Search on PubMed
DOI: 10.1021/acs.jmedchem.0c01652
Primary Citation of Related Structures:
7K6M, 7K6N, 7K6O, 7K71

PubMed Abstract:

Macromolecules

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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P42336
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
VXY (Subject of Investigation/LOI) Query on VXY Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	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		Ligand Interaction

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
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 = 59.038	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

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2021-01-06

Deposition Author(s):

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

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.