5I4U | pdb_00005i4u

The crystal structure of PI3Kdelta with compound 34

PDB DOI: https://doi.org/10.2210/pdb5I4U/pdb

Classification: TRANSFERASE/TRANSFERASE INHIBITOR
Organism(s): Mus musculus
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2016-02-12 Released: 2017-02-22
Deposition Author(s): Somoza, J.R., Villasenor, A.G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.37 Å
R-Value Free:
0.290 (Depositor), 0.290 (DCC)
R-Value Work:
0.222 (Depositor), 0.230 (DCC)
R-Value Observed:
0.226 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

The Design and Synthesis of Potent, Selective and Metabolically Stable PI3K[delta] Inhibitors

Somoza, J.R., Villasenor, G.A.

To be published.

Macromolecule Content

Total Structure Weight: 108.2 kDa
Atom Count: 6,681
Modeled Residue Count: 815
Deposited Residue Count: 939
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	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% 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
67T Query on 67T 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-{[(1S)-1-(5-chloro-4-oxo-3-phenyl-3,4-dihydroquinazolin-2-yl)ethyl]amino}pyrimidine-5-carbonitrile C₂₁ H₁₇ Cl N₈ O QQBVZBSMGUVONA-NSHDSACASA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
67T	BindingDB: 5I4U	IC50: 0.1 (nM) from 1 assay(s)
67T	BindingDB: 5I4U	EC50: 0.3 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.37 Å
R-Value Free: 0.290 (Depositor), 0.290 (DCC)
R-Value Work: 0.222 (Depositor), 0.230 (DCC)
R-Value Observed: 0.226 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.272	α = 90
b = 143.482	β = 90
c = 221.053	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2017-02-22

Deposition Author(s):

Villasenor, A.G.

Revision History (Full details and data files)

Version 1.0: 2017-02-22
Type: Initial release
Version 1.1: 2023-09-27
Changes: Data collection, Database references, Refinement description

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.