5NGB | pdb_00005ngb

X-Ray Diffraction Crystal Structure of the murine PI3K p110delta in complex with a pan inhibitor

• PDB DOI: https://doi.org/10.2210/pdb5NGB/pdb

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


• Deposited: 2017-03-17 Released: 2017-09-13 
• Deposition Author(s): Berndt, A., Williams, R.L.
• Funding Organization(s): Medical Research Council (United Kingdom)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 
  0.290 (Depositor), 0.288 (DCC) 
• R-Value Work: 
  0.242 (Depositor), 0.243 (DCC) 
• R-Value Observed: 
  0.245 (Depositor) 

Starting Model: experimental

Literature

Identification of a Potent Phosphoinositide 3-Kinase Pan Inhibitor Displaying a Strategic Carboxylic Acid Group and Development of Its Prodrugs.

Pirali, T., Ciraolo, E., Aprile, S., Massarotti, A., Berndt, A., Griglio, A., Serafini, M., Mercalli, V., Landoni, C., Campa, C.C., Margaria, J.P., Silva, R.L., Grosa, G., Sorba, G., Williams, R., Hirsch, E., Tron, G.C.

(2017) ChemMedChem 12: 1542-1554

• PubMed: 28857471 
• DOI: https://doi.org/10.1002/cmdc.201700340
• Primary Citation Related Structures: 
  5NGB


• PubMed Abstract: 
  

  Activation of the phosphoinositide 3-kinase (PI3K) pathway is a key signaling event in cancer, inflammation, and other proliferative diseases. PI3K inhibitors are already approved for some specific clinical indications, but their systemic on-target toxicity limits their larger use. In particular, whereas toxicity is tolerable in acute treatment of life-threatening diseases, this is less acceptable in chronic conditions. In the past, the strategy to overcome this drawback was to block selected isoforms mainly expressed in leukocytes, but redundancy within the PI3K family members challenges the effectiveness of this approach. On the other hand, decreasing exposure to selected target cells represents a so-far unexplored alternative to circumvent systemic toxicity. In this manuscript, we describe the generation of a library of triazolylquinolones and the development of the first prodrug pan-PI3K inhibitor.

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Organizational Affiliation: 
• Dipartimento di Scienze del Farmaco, Università degli Studi del Piemonte Orientale "A. Avogadro", Largo Donegani 2, 28100, Novara, Italy.
Department of Molecular Biotechnology and Health Sciences, University of Torino, Via Nizza 52, 10126, Torino, Italy.
MRC Laboratory of Molecular Biology, Medical Research Council, Cambridge, CB2 0QH, UK.
Department of Pharmacology, Ribeirão Preto Medical School, University of São Paulo, Avenida Bandeirantes 3900, 14049-900, Ribeirão Preto, Brazil.
Kither Biotech S.r.l., Molecular Biotechnology Center, Via Nizza 52, 10126, Torino, Italy.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 124.74 kDa 
• Atom Count: 6,625 
• Modeled Residue Count: 816 
• Deposited Residue Count: 1,079 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit delta isoform	A	1,079	Mus musculus	Mutation(s): 0  Gene Names: Pik3cd EC: 2.7.1.137 (UniProt), 2.7.1.153 (UniProt)
UniProt
Find proteins for O35904 (Mus musculus) Explore O35904  Go to UniProtKB:  O35904

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
8WH	B [auth A]	3-[[4-(2-morpholin-4-yl-4-oxidanylidene-3~{H}-quinolin-8-yl)-1,2,3-triazol-1-yl]methyl]benzoic acid C23 H21 N5 O4 PJYOPNLTNBDQPR-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free:  0.290 (Depositor), 0.288 (DCC) 
• R-Value Work:  0.242 (Depositor), 0.243 (DCC) 
• R-Value Observed: 0.245 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.437	α = 90
b = 143.586	β = 90
c = 220.193	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-09-13 
Deposition Author(s): Berndt, A., Williams, R.L.

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Funding Organization	Location	Grant Number
Medical Research Council (United Kingdom)	United Kingdom	MC_U105184308

Revision History  

• Version 1.0: 2017-09-13
  Type: Initial release
  
• Version 1.1: 2017-09-27
  Changes: Database references
• Version 1.2: 2019-02-20
  Changes: Advisory, Data collection, Derived calculations
• Version 1.3: 2024-01-17
  Changes: Data collection, Database references, Refinement description