5T7F

PI3Kdelta in complex with the inhibitor GS-643624

PDB DOI: https://doi.org/10.2210/pdb5T7F/pdb

Classification: Transferase/Transferase Inhibitor
Organism(s): Mus musculus
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2016-09-04 Released: 2016-12-28
Deposition Author(s): Somoza, J.R., Villasenor, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.294
R-Value Work: 0.230
R-Value Observed: 0.230

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

The Discovery of GS-9901: A Potent, Selective and Metabolically Stable Inhibitor of PI3Kd

Patel, L., Chandrasekhar, J., Evarts, J., Forseth, K., Haran, A., Ip, C., Kashishian, A., Kim, M., Koditek, D., Koppenol, S., Lad, L., Lepist, E.-I., McGrath, M.E., Perreault, S., Puri, K., Villasenor, A., Somoza, J.R., Steiner, B., Therrien, J., Trilberg, J., Phillips, G.

To be published.

Macromolecule Content

Total Structure Weight: 216.46 kDa
Atom Count: 13,339
Modelled Residue Count: 1,635
Deposited Residue Count: 1,878
Unique protein chains: 1

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 delta isoform	A, B	939	Mus musculus	Mutation(s): 0 Gene Names: Pik3cd EC: 2.7.1.153
UniProt
Find proteins for O35904 (Mus musculus) Explore O35904 Go to UniProtKB: O35904
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O35904
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
76C Query on 76C Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B]	C [auth A], D [auth B]	2,4-bis(azanyl)-6-[[(1~{S})-1-[5-chloranyl-3-(5-fluoranyl-4-methyl-pyridin-3-yl)-4-oxidanylidene-quinazolin-2-yl]ethyl]amino]pyrimidine-5-carbonitrile C₂₁ H₁₇ Cl F N₉ O UISOZEPWNXYPCK-JTQLQIEISA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
76C	BindingDB: 5T7F	IC50: min: 0.3, max: 40 (nM) from 4 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.294
R-Value Work: 0.230
R-Value Observed: 0.230
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.226	α = 90
b = 142.794	β = 90.055
c = 221.067	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
EPMR	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2016-12-28

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-12-28
Type: Initial release
Version 1.1: 2024-03-06
Changes: Data collection, 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.