3R7Q

Structure-based design of thienobenzoxepin inhibitors of PI3- kinase

• PDB DOI: https://doi.org/10.2210/pdb3R7Q/pdb

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


• Deposited: 2011-03-22 Released: 2011-08-03 
• Deposition Author(s): Murray, J.M., Wiesmann, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.269 
• R-Value Work: 0.216 
• R-Value Observed: 0.219 

Starting Model: experimental

Literature

Structure-based design of thienobenzoxepin inhibitors of PI3-kinase.

Staben, S.T., Siu, M., Goldsmith, R., Olivero, A.G., Do, S., Burdick, D.J., Heffron, T.P., Dotson, J., Sutherlin, D.P., Zhu, B.Y., Tsui, V., Le, H., Lee, L., Lesnick, J., Lewis, C., Murray, J.M., Nonomiya, J., Pang, J., Prior, W.W., Salphati, L., Rouge, L., Sampath, D., Sideris, S., Wiesmann, C., Wu, P.

(2011) Bioorg Med Chem Lett 21: 4054-4058

• PubMed: 21636270 
• DOI: https://doi.org/10.1016/j.bmcl.2011.04.124
• Primary Citation of Related Structures:  
  3R7Q, 3R7R


• PubMed Abstract: 
  

  Starting from thienobenzopyran HTS hit 1, co-crystallization, molecular modeling and metabolic analysis were used to design potent and metabolically stable inhibitors of PI3-kinase. Compound 15 demonstrated PI3K pathway suppression in a mouse MCF7 xenograft model.

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Organizational Affiliation: 

Discovery Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA. [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: 111.08 kDa 
• Atom Count: 6,800 
• Modelled Residue Count: 837 
• 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
FAV	B [auth A]	N-(2-chlorophenyl)-N-methyl-4H-thieno[3,2-c]chromene-2-carboxamide C19 H14 Cl N O2 S PCSYEOAUKWBYOX-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
FAV	PDBBind:  3R7Q	IC50: 108 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.269 
• R-Value Work: 0.216 
• R-Value Observed: 0.219 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 141.782	α = 90
b = 67.494	β = 96.43
c = 105.892	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-08-03 
Deposition Author(s): Murray, J.M., Wiesmann, C.

Revision History  

• Version 1.0: 2011-08-03
  Type: Initial release
  
• Version 1.1: 2012-09-05
  Changes: Database references
• Version 1.2: 2019-07-17
  Changes: Data collection, Refinement description
• Version 1.3: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description