3ZVV | pdb_00003zvv

Fragment Bound to PI3Kinase gamma

• PDB DOI: https://doi.org/10.2210/pdb3ZVV/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: unidentified baculovirus
• Mutation(s): No 


• Deposited: 2011-07-27 Released: 2011-09-28 
• Deposition Author(s): Hughes, S.J., Milan, D.S., Kilty, I.C., Lewthwaite, R.A., Mathias, J.P., O'Reilly, M.A., Phelan, A., Baldock, D.A., Brown, D.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.242 (Depositor), 0.255 (DCC) 
• R-Value Work: 
  0.192 (Depositor), 0.203 (DCC) 
• R-Value Observed: 
  0.194 (Depositor) 

Literature

Fragment based discovery of a novel and selective PI3 kinase inhibitor.

Hughes, S.J., Millan, D.S., Kilty, I.C., Lewthwaite, R.A., Mathias, J.P., O'Reilly, M.A., Pannifer, A., Phelan, A., Stuhmeier, F., Baldock, D.A., Brown, D.G.

(2011) Bioorg Med Chem Lett 21: 6586-6590

• PubMed: 21925880 
• DOI: https://doi.org/10.1016/j.bmcl.2011.07.117
• Primary Citation Related Structures: 
  3ZVV, 3ZW3


• PubMed Abstract: 
  

  We report the use of fragment screening and fragment based drug design to develop a PI3γ kinase fragment hit into a lead. Initial fragment hits were discovered by high concentration biochemical screening, followed by a round of virtual screening to identify additional ligand efficient fragments. These were developed into potent and ligand efficient lead compounds using structure guided fragment growing and merging strategies. This led to a potent, selective, and cell permeable PI3γ kinase inhibitor with good metabolic stability that was useful as a preclinical tool compound.

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Organizational Affiliation: 
• Worldwide Medicinal Chemistry, Pfizer Global Research and Development, Sandwich Laboratories, Ramsgate Road, Sandwich, Kent CT13 9NJ, 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: 110.89 kDa 
• Atom Count: 7,023 
• Modeled Residue Count: 829 
• 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  EC: 2.7.1.137 (PDB Primary Data), 2.7.1.153 (PDB Primary Data), 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
XAZ	B [auth A]	5,7-dimethylpyrazolo[1,5-a]pyrimidin-2-amine C8 H10 N4 JTTOBYJUZIFSFJ-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
XAZ	BindingDB:  3ZVV	IC50: 9.15e+5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.242 (Depositor), 0.255 (DCC) 
• R-Value Work:  0.192 (Depositor), 0.203 (DCC) 
• R-Value Observed: 0.194 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 143.488	α = 90
b = 68.031	β = 95.16
c = 106.251	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-09-28 
Deposition Author(s): Hughes, S.J., Milan, D.S., Kilty, I.C., Lewthwaite, R.A., Mathias, J.P., O'Reilly, M.A., Phelan, A., Baldock, D.A., Brown, D.G.

Revision History  

• Version 1.0: 2011-09-28
  Type: Initial release
  
• Version 1.1: 2011-10-19
  Changes: Database references, Other
• Version 1.2: 2018-02-07
  Changes: Database references, Source and taxonomy, Structure summary
• Version 1.3: 2024-05-08
  Changes: Data collection, Database references, Derived calculations, Other