5I6U | pdb_00005i6u

The crystal structure of PI3Kdelta with compound 32

PDB DOI: https://doi.org/10.2210/pdb5I6U/pdb

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

Deposited: 2016-02-16 Released: 2017-02-22
Deposition Author(s): Somoza, J.R., Villasenor, A.G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.84 Å
R-Value Free:
0.307 (Depositor), 0.310 (DCC)
R-Value Work:
0.212 (Depositor), 0.220 (DCC)
R-Value Observed:
0.220 (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 crystal structure of PI3Kdelta with compound 32

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

To be published.

Macromolecule Content

Total Structure Weight: 108.25 kDa
Atom Count: 6,622
Modeled Residue Count: 816
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
68R Query on 68R 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-[(1S)-1-({6-amino-5-[(1H-pyrazol-4-yl)ethynyl]pyrimidin-4-yl}amino)ethyl]-5-chloro-3-phenylquinazolin-4(3H)-one C₂₅ H₁₉ Cl N₈ O QSVWZWFVMMFIJE-HNNXBMFYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
68R	BindingDB: 5I6U	IC50: min: 0.3, max: 100 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.84 Å
R-Value Free: 0.307 (Depositor), 0.310 (DCC)
R-Value Work: 0.212 (Depositor), 0.220 (DCC)
R-Value Observed: 0.220 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 142.836	α = 90
b = 64.926	β = 103.172
c = 117.058	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data reduction
HKL-2000	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.