4XIP

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: 1.7 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.201 

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 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
40W
Query on 40W

Download SDF File 
Download CCD File 
A
4-(3,6,6-trimethyl-4-oxo-4,5,6,7-tetrahydro-1H-indol-1-yl)benzamide
C18 H20 N2 O2
WCNWRBAQSUPKHE-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
40WKi: 235 nM (100) BINDINGDB
40WKi: 235 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.201 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 66.882α = 90.00
b = 90.929β = 90.00
c = 98.955γ = 90.00
Software Package:
Software NamePurpose
BUSTERrefinement
PROCESSdata reduction
PROCESSdata scaling
BUSTERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



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