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), 0.293 (DCC)
R-Value Work:
0.222 (Depositor), 0.229 (DCC)
R-Value Observed:
0.226 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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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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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
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), 0.293 (DCC)
R-Value Work: 0.222 (Depositor), 0.229 (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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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

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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.