3T8M | pdb_00003t8m

Rational Design of PI3K-alpha Inhibitors that Exhibit Selectivity Over the PI3K-beta Isoform

PDB DOI: https://doi.org/10.2210/pdb3T8M/pdb

Classification: TRANSFERASE/TRANSFERASE INHIBITOR
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2011-08-01 Released: 2011-11-16
Deposition Author(s): Murray, J.M., Wiesmann, C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.254 (Depositor), 0.252 (DCC)
R-Value Work:
0.204 (Depositor), 0.202 (DCC)
R-Value Observed:
0.207 (Depositor)

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Rational Design of PI3K-alpha Inhibitors that Exhibit Selectivity Over the PI3K-beta Isoform

Heffron, T., Wei, B., Olivero, A.G., Staben, S.T., Tsui, V., Do, S., Dotson, J., Folkes, A., Goldsmith, A., Goldsmith, R., Gunzner, J., Lesnick, J., Lewis, C., Mathieu, S., Nonomiya, J., Sutherlin, D.P., Wan, N.C., Wang, S., Weismann, C., Zhu, B.

To be published.

Macromolecule Content

Total Structure Weight: 111.28 kDa
Atom Count: 6,865
Modeled Residue Count: 841
Deposited Residue Count: 966
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit gamma isoform	A	966	Homo sapiens	Mutation(s): 0 Gene Names: PIK3CG EC: 2.7.1.153 (PDB Primary Data), 2.7.1.137 (UniProt), 2.7.1.154 (UniProt), 2.7.11.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P48736 (Homo sapiens) Explore P48736 Go to UniProtKB: P48736
PHAROS: P48736 GTEx: ENSG00000105851
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P48736
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
3T8 Query on 3T8 Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	N~2~-{2-chloro-4-[(4-methylpiperazin-1-yl)carbonyl]phenyl}-N~2~,N~8~-dimethyl-4,5-dihydrothieno[3,2-d][1]benzoxepine-2,8-dicarboxamide C₂₈ H₂₉ Cl N₄ O₄ S TVUWQOATJJJPPP-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.254 (Depositor), 0.252 (DCC)
R-Value Work: 0.204 (Depositor), 0.202 (DCC)
R-Value Observed: 0.207 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 143.219	α = 90
b = 67.651	β = 95.55
c = 106.627	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection

Structure Validation

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Entry History

Deposition Data

Released Date: 2011-11-16

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-11-16
Type: Initial release
Version 1.1: 2017-11-08
Changes: Refinement description
Version 1.2: 2024-02-28
Changes: Data collection, Database references, Derived calculations

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.