Biological Assembly 1  

 3D View: Structure | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 28.37 kDa 
• Atom Count: 1993 
• Modelled Residue Count: 221 
• Deposited Residue Count: 249 
• Unique protein chains: 1

2XJX

Structure of HSP90 with small molecule inhibitor bound

• DOI: 10.2210/pdb2XJX/pdb

• Classification: CHAPERONE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-07-06 Released: 2010-08-11 
• Deposition Author(s): Murray, C.W., Carr, M.G., Callaghan, O., Chessari, G., Congreve, M., Cowan, S., Coyle, J.E., Downham, R., Figueroa, E., Frederickson, M., Graham, B., McMenamin, R., OBrien, M.A., Patel, S., Phillips, T.R., Williams, G., Woodhead, A.J., Woolford, A.J.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.66 Å
• R-Value Free: 0.208 
• R-Value Work: 0.155 
• R-Value Observed: 0.158 

Literature

Discovery of (2,4-Dihydroxy-5-Isopropylphenyl)-[5-(4-Methylpiperazin-1-Ylmethyl)-1,3-Dihydroisoindol-2-Yl]Methanone (at13387), a Novel Inhibitor of the Molecular Chaperone Hsp90 by Fragment Based Drug Design.

Woodhead, A.J., Angove, H., Carr, M.G., Chessari, G., Congreve, M., Coyle, J.E., Cosme, J., Graham, B., Day, P.J., Downham, R., Fazal, L., Feltell, R., Figueroa, E., Frederickson, M., Lewis, J., Mcmenamin, R., Murray, C.W., O'Brien, M.A., Parra, L., Patel, S., Phillips, T., Rees, D.C., Rich, S., Smith, D.M., Trewartha, G., Vinkovic, M., Williams, B., Woolford, A.J.

(2010) J Med Chem 53: 5956

• PubMed: 20662534 
• DOI: 10.1021/jm100060b
• Primary Citation of Related Structures:  
  2XAB, 2XJG, 2XJJ, 2XJX


• PubMed Abstract: 
  

Inhibitors of the molecular chaperone heat shock protein 90 (Hsp90) are currently generating significant interest in clinical development as potential treatments for cancer. In a preceding publication (DOI: 10.1021/jm100059d ) we describe Astex's approach to screening fragments against Hsp90 and the subsequent optimization of two hits into leads with inhibitory activities in the low nanomolar range. This paper describes the structure guided optimization of the 2,4-dihydroxybenzamide lead molecule 1 and details some of the drug discovery strategies employed in the identification of AT13387 (35), which has progressed through preclinical development and is currently being tested in man.

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Organizational Affiliation: 

Medicinal Chemistry, Astex Therapeutics, Ltd., Cambridge, UK. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HEAT SHOCK PROTEIN HSP 90-ALPHA	A	249	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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
XJX (Subject of Investigation/LOI)	B [auth A]	Onalespib C24 H31 N3 O3 IFRGXKKQHBVPCQ-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
XJX	Binding MOAD:  2XJX	Kd: 0.71 (nM) from 1 assay(s)
	PDBBind:  2XJX	Kd: 0.71 (nM) from 1 assay(s)
	BindingDB:  2XJX	IC50: min: 14, max: 350 (nM) from 6 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.66 Å
• R-Value Free: 0.208 
• R-Value Work: 0.155 
• R-Value Observed: 0.158 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.95	α = 90
b = 41.05	β = 101.86
c = 49.23	γ = 90

Software Package:

Software Name	Purpose
BUSTER-TNT	refinement

Structure Validation

Ligand Structure Quality Assessment  

Entry History 

Deposition Data

• Deposited Date: 2010-07-06 
• Released Date: 2010-08-11 
Deposition Author(s): Murray, C.W., Carr, M.G., Callaghan, O., Chessari, G., Congreve, M., Cowan, S., Coyle, J.E., Downham, R., Figueroa, E., Frederickson, M., Graham, B., McMenamin, R., OBrien, M.A., Patel, S., Phillips, T.R., Williams, G., Woodhead, A.J., Woolford, A.J.A.

Revision History  

• Version 1.0: 2010-08-11
  Type: Initial release
  
• Version 1.1: 2013-04-24
  Changes: Other, Structure summary, Version format compliance
• Version 1.2: 2015-02-18
  Changes: Non-polymer description, Structure summary