4XIQ

Discovery of novel oxazepine and diazepine carboxamides as two new classes of heat shock protein 90 inhibitors

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.192 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

Discovery of novel oxazepine and diazepine carboxamides as two new classes of heat shock protein 90 inhibitors.

Neubert, T., Numa, M., Ernst, J., Clemens, J., Krenitsky, P., Liu, M., Fleck, B., Woody, L., Zuccola, H., Stamos, D.

(2015) Bioorg.Med.Chem.Lett. 25: 1338-1342

  • DOI: 10.1016/j.bmcl.2015.01.023
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • Two novel series of oxazepine and diazepine based HSP90 inhibitors are reported. This effort relied on structure based design and isothermal calorimetry to identify small drug like macrocycles. Computational modelling was used to build into a solvent ...

    Two novel series of oxazepine and diazepine based HSP90 inhibitors are reported. This effort relied on structure based design and isothermal calorimetry to identify small drug like macrocycles. Computational modelling was used to build into a solvent exposed pocket near the opening of the ATP binding site, which led to potent inhibitors of HSP90 (25-30).

    Organizational Affiliation: 

    Vertex Pharmaceuticals Incorporated, Department of Structural Biology, 50 Northern Avenue, Boston, MA 02210, United States.,Vertex Pharmaceuticals Incorporated, Department of Chemistry, 11010 Torreyana Road, San Diego, CA 92121, United States.,Vertex Pharmaceuticals Incorporated, Department of Biology, 11010 Torreyana Road, San Diego, CA 92121, United States.,Vertex Pharmaceuticals Incorporated, Department of Chemistry, 11010 Torreyana Road, San Diego, CA 92121, United States. Electronic address: timothy_neubert@vrtx.com.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Heat shock protein HSP 90-alpha
A
233Homo sapiensMutation(s): 0 
Gene Names: HSP90AA1 (HSP90A, HSPC1, HSPCA)
Find proteins for P07900 (Homo sapiens)
Go to Gene View: HSP90AA1
Go to UniProtKB:  P07900
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
40Y
Query on 40Y
Download SDF File 
Download CCD File 
A
8,11,11-trimethyl-9-oxo-6,7,9,10,11,12-hexahydroindolo[2,1-d][1,5]benzoxazepine-3-carboxamide
C20 H22 N2 O3
CXFXSTHDYJQJAP-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL
Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
40YKi: 86 nM (100) BINDINGDB
40YKi: 86 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.192 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 66.837α = 90.00
b = 90.977β = 90.00
c = 99.056γ = 90.00
Software Package:
Software NamePurpose
BUSTERrefinement
PROCESSdata reduction
BUSTERphasing
PROCESSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-03-04
    Type: Initial release
  • Version 1.1: 2015-04-01
    Type: Database references
  • Version 1.2: 2016-06-01
    Type: Data collection