3DPD | pdb_00003dpd

Achieving multi-isoform PI3K inhibition in a series of substituted 3,4-Dihydro-2H-benzo[1,4]oxazines

• PDB DOI: https://doi.org/10.2210/pdb3DPD/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2008-07-08 Released: 2008-08-26 
• Deposition Author(s): Ceska, T.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• R-Value Free: 
  0.318 (Depositor), 0.246 (DCC) 
• R-Value Work: 
  0.242 (Depositor), 0.240 (DCC) 

Starting Model: experimental

Literature

Achieving multi-isoform PI3K inhibition in a series of substituted 3,4-dihydro-2H-benzo[1,4]oxazines

Perry, B., Alexander, R., Bennett, G., Buckley, G., Ceska, T., Crabbe, T., Dale, V., Gowers, L., Horsley, H., James, L., Jenkins, K., Crepy, K., Kulisa, C., Lightfoot, H., Lock, C., Mack, S., Morgan, T., Nicolas, A.-L., Pitt, W., Sabin, V., Wright, S.

(2008) Bioorg Med Chem Lett 18: 4700-4704

• PubMed: 18644721 
• DOI: https://doi.org/10.1016/j.bmcl.2008.06.104
• Primary Citation of Related Structures:  
  3DPD


• PubMed Abstract: 
  

  The SAR and pharmacokinetic profiles of a series of multi-isoform PI3K inhibitors based on a 3,4-dihydro-2H-benzo[1,4]oxazine scaffold are disclosed.

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Organizational Affiliation: 
• UCB, Medicinal Chemistry, Granta Park, Great Abington, Cambridge CB21 6GS, UK. [e-mail]

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: 111.02 kDa 
• Atom Count: 6,879 
• Modeled Residue Count: 846 
• Deposited Residue Count: 966 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit gamma isoform	A	966	Homo sapiens	Mutation(s): 0  Gene Names: PIK3CG EC: 2.7.1.153 (PDB Primary Data), 2.7.1.137 (UniProt), 2.7.1.154 (UniProt), 2.7.11.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P48736 (Homo sapiens) Explore P48736  Go to UniProtKB:  P48736
PHAROS:  P48736 GTEx:  ENSG00000105851

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
41A	B [auth A]	5,5-dimethyl-2-morpholin-4-yl-5,6-dihydro-1,3-benzothiazol-7(4H)-one C13 H18 N2 O2 S DZXMARZBAUMWLK-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
41A	BindingDB:  3DPD	IC50: min: 1660, max: 3453 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• R-Value Free:  0.318 (Depositor), 0.246 (DCC) 
• R-Value Work:  0.242 (Depositor), 0.240 (DCC) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 142.23	α = 90
b = 67.77	β = 95.96
c = 105.87	γ = 90

Software Package:

Software Name	Purpose
SCALA	data processing
CNS	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
MOSFLM	data reduction
SCALA	data scaling
CNS	phasing
CNX	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-08-26 
Deposition Author(s): Ceska, T.A.

Revision History  

• Version 1.0: 2008-08-26
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2025-04-30
  Changes: Structure summary