Structure-based design of thienobenzoxepin inhibitors of PI3- kinase

Experimental Data Snapshot

  • Resolution: 2.50 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.219 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


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

  • 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.

  • Organizational Affiliation

    Discovery Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA. stevents@gene.com

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit gamma isoform966Homo sapiensMutation(s): 0 
Gene Names: PIK3CG
UniProt & NIH Common Fund Data Resources
Find proteins for P48736 (Homo sapiens)
Explore P48736 
Go to UniProtKB:  P48736
GTEx:  ENSG00000105851 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP48736
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on FAV

Download Ideal Coordinates CCD File 
B [auth A]N-(2-chlorophenyl)-N-methyl-4H-thieno[3,2-c]chromene-2-carboxamide
C19 H14 Cl N O2 S
Binding Affinity Annotations 
IDSourceBinding Affinity
FAV PDBBind:  3R7Q IC50: 108 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • 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 = 141.782α = 90
b = 67.494β = 96.43
c = 105.892γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
DENZOdata reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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