5T8I | pdb_00005t8i

PI3Kdelta in complex with the inhibitor GS-9901

PDB DOI: https://doi.org/10.2210/pdb5T8I/pdb

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

Deposited: 2016-09-07 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:
0.313 (Depositor), 0.316 (DCC)
R-Value Work:
0.252 (Depositor), 0.258 (DCC)
R-Value Observed:
0.256 (Depositor)

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Ligand Structure Quality Assessment

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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: 108.24 kDa
Atom Count: 6,562
Modeled Residue Count: 808
Deposited Residue Count: 939
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 delta isoform	A	939	Mus musculus	Mutation(s): 0 Gene Names: Pik3cd EC: 2.7.1.153 (PDB Primary Data), 2.7.1.137 (UniProt)
UniProt
Find proteins for O35904 (Mus musculus) Explore O35904 Go to UniProtKB: O35904
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O35904
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
77C Query on 77C 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]	2,4-diamino-6-{[(S)-[5-chloro-8-fluoro-4-oxo-3-(pyridin-3-yl)-3,4-dihydroquinazolin-2-yl](cyclopropyl)methyl]amino}pyrimidine-5-carbonitrile C₂₂ H₁₇ Cl F N₉ O XDSXYMOZKDUASY-INIZCTEOSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
77C	BindingDB: 5T8I	IC50: 1 (nM) from 1 assay(s)
77C	BindingDB: 5T8I	EC50: min: 0.31, max: 2.4 (nM) from 4 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.313 (Depositor), 0.316 (DCC)
R-Value Work: 0.252 (Depositor), 0.258 (DCC)
R-Value Observed: 0.256 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.045	α = 90
b = 142.197	β = 90
c = 222.59	γ = 90

Software Package:

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

Structure Validation

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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

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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.