3BM9

Discovery of Benzisoxazoles as Potent Inhibitors of Chaperone Hsp90

• PDB DOI: https://doi.org/10.2210/pdb3BM9/pdb

• Classification: CHAPERONE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-12-12 Released: 2008-07-08 
• Deposition Author(s): Gopalsamy, A., Shi, M., Vogan, E.M., Golas, J., Jacob, J., Johnson, J., Lee, F., Nilakantan, R., Peterson, R., Svenson, K., Tam, M.S., Wen, Y., Chopra, R., Ellingboe, J., Arndt, K., Boschelli, F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.186 
• R-Value Work: 0.164 
• R-Value Observed: 0.165 

Literature

Discovery of benzisoxazoles as potent inhibitors of chaperone heat shock protein 90.

Gopalsamy, A., Shi, M., Golas, J., Vogan, E., Jacob, J., Johnson, M., Lee, F., Nilakantan, R., Petersen, R., Svenson, K., Chopra, R., Tam, M.S., Wen, Y., Ellingboe, J., Arndt, K., Boschelli, F.

(2008) J Med Chem 51: 373-375

• PubMed: 18197612 
• DOI: https://doi.org/10.1021/jm701385c
• Primary Citation of Related Structures:  
  3BM9, 3BMY


• PubMed Abstract: 
  

  Heat shock protein 90 (Hsp90) is a molecular chaperone that is responsible for activating many signaling proteins and is a promising target in tumor biology. We have identified small-molecule benzisoxazole derivatives as Hsp90 inhibitors. Crystallographic studies show that these compounds bind in the ATP binding pocket interacting with the Asp93. Structure based optimization led to the identification of potent analogues, such as 13, with good biochemical profiles.

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Organizational Affiliation: 

Chemical and Screening Sciences, Wyeth Research, Pearl River, NY 10965, USA. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 25.73 kDa 
• Atom Count: 2,036 
• Modelled Residue Count: 207 
• Deposited Residue Count: 226 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Heat shock protein HSP 90-alpha	A	226	Homo sapiens	Mutation(s): 0  Gene Names: HSP90AA1, HSP90A, HSPC1, HSPCA EC: 3.6.4.10
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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BXZ	B [auth A]	4-bromo-6-(6-hydroxy-1,2-benzisoxazol-3-yl)benzene-1,3-diol C13 H8 Br N O4 LZACPHWPRDKUPK-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
BXZ	BindingDB:  3BM9	IC50: 190 (nM) from 1 assay(s)
	PDBBind:  3BM9	IC50: 190 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.186 
• R-Value Work: 0.164 
• R-Value Observed: 0.165 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.089	α = 90
b = 89.033	β = 90
c = 100.172	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
StructureStudio	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-07-08 
Deposition Author(s): Gopalsamy, A., Shi, M., Vogan, E.M., Golas, J., Jacob, J., Johnson, J., Lee, F., Nilakantan, R., Peterson, R., Svenson, K., Tam, M.S., Wen, Y., Chopra, R., Ellingboe, J., Arndt, K., Boschelli, F.

Revision History  

• Version 1.0: 2008-07-08
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-02-21
  Changes: Data collection, Database references, Derived calculations