4XIQ

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

• PDB DOI: https://doi.org/10.2210/pdb4XIQ/pdb

• Classification: Chaperone/chaperone Inhibitor
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2015-01-07 Released: 2015-03-04 
• Deposition Author(s): Neubert, T., Zuccola, H.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.84 Å
• R-Value Free: 0.206 
• R-Value Work: 0.192 
• R-Value Observed: 0.193 

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

• PubMed: 25677667 
• DOI: https://doi.org/10.1016/j.bmcl.2015.01.023
• Primary Citation of Related Structures:  
  4XIP, 4XIQ, 4XIR, 4XIT


• 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 exposed pocket near the opening of the ATP binding site, which led to potent inhibitors of HSP90 (25-30).

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Organizational Affiliation: 

Vertex Pharmaceuticals Incorporated, Department of Chemistry, 11010 Torreyana Road, San Diego, CA 92121, United States. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 26.71 kDa 
• Atom Count: 1,866 
• Modelled Residue Count: 209 
• Deposited Residue Count: 233 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Heat shock protein HSP 90-alpha	A	233	Homo sapiens	Mutation(s): 0  Gene Names: HSP90AA1, HSP90A, HSPC1, HSPCA
UniProt & NIH Common Fund Data Resources
Find proteins for P07900 (Homo sapiens) Explore P07900  Go to UniProtKB:  P07900
PHAROS:  P07900 GTEx:  ENSG00000080824

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
40Y	B [auth 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
GOL	C [auth A], D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
40Y	BindingDB:  4XIQ	Ki: 86 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.84 Å
• R-Value Free: 0.206 
• R-Value Work: 0.192 
• R-Value Observed: 0.193 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.837	α = 90
b = 90.977	β = 90
c = 99.056	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
PROCESS	data reduction
PROCESS	data scaling
BUSTER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-03-04 
Deposition Author(s): Neubert, T., Zuccola, H.J.

Revision History  

• Version 1.0: 2015-03-04
  Type: Initial release
  
• Version 1.1: 2015-04-01
  Changes: Database references
• Version 1.2: 2016-06-01
  Changes: Data collection
• Version 1.3: 2024-02-28
  Changes: Data collection, Database references, Derived calculations