Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 25.85 kDa 
• Atom Count: 2029 
• Modelled Residue Count: 208 
• Deposited Residue Count: 226 
• Unique protein chains: 1

3R92

Discovery of a macrocyclic o-aminobenzamide Hsp90 inhibitor with heterocyclic tether that shows extended biomarker activity and in vivo efficacy in a mouse xenograft model.

• PDB DOI: 10.2210/pdb3R92/pdb

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


• Deposited: 2011-03-24 Released: 2011-06-08 
• Deposition Author(s): Zapf, C.W., Bloom, J.D., McBean, J.L., Dushin, R.G., Golas, J.M., Liu, H., Lucas, J., Boschelli, F., Vogan, E.M., Levin, J.I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.58 Å
• R-Value Free: 0.194 
• R-Value Work: 0.176 
• R-Value Observed: 0.177 

Literature

Discovery of a macrocyclic o-aminobenzamide Hsp90 inhibitor with heterocyclic tether that shows extended biomarker activity and in vivo efficacy in a mouse xenograft model.

Zapf, C.W., Bloom, J.D., McBean, J.L., Dushin, R.G., Golas, J.M., Liu, H., Lucas, J., Boschelli, F., Vogan, E., Levin, J.I.

(2011) Bioorg Med Chem Lett 21: 3627-3631

• PubMed: 21605975 
• DOI: 10.1016/j.bmcl.2011.04.102
• Primary Citation of Related Structures:  
  3R92


• PubMed Abstract: 
  

A novel series of macrocyclic ortho-aminobenzamide Hsp90 inhibitors is reported. In continuation of our research, heterocycle-containing tethers were explored with the intent to further improve potency and minimize hERG liabilities. This effort culminated in the discovery of compound 10, which efficiently suppressed proliferation of HCT116 and U87 cells. This compound showed prolonged Hsp90-inhibitory activity at least 24h post-administration consistent with elevated and prolonged exposure in the tumor. When studied in a xenograft model, the compound demonstrated significant suppression of tumor growth.

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Organizational Affiliation: 

Medicinal Chemistry, Pfizer, Pearl River, NY 10965, United States. [e-mail]

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: HSP90A, HSP90AA1, 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
06J	B [auth A]	(3aR)-13,13,16-trimethyl-15-oxo-1,2,3,3a,4,5,12,14,15,17,18,19-dodecahydro-13H-10,6-(metheno)pyrrolo[2',1':3,4][1,4,9]triazacyclotetradecino[9,8-a]indole-7-carboxamide C26 H34 N4 O2 WQTXERXALASGRT-GOSISDBHSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
06J	Binding MOAD:  3R92	IC50: 883 (nM) from 1 assay(s)
	BindingDB:  3R92	IC50: 96 (nM) from 1 assay(s)
	PDBBind:  3R92	IC50: 96 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.58 Å
• R-Value Free: 0.194 
• R-Value Work: 0.176 
• R-Value Observed: 0.177 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.35	α = 90
b = 90.355	β = 90
c = 98.594	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-03-24 
• Released Date: 2011-06-08 
Deposition Author(s): Zapf, C.W., Bloom, J.D., McBean, J.L., Dushin, R.G., Golas, J.M., Liu, H., Lucas, J., Boschelli, F., Vogan, E.M., Levin, J.I.

Revision History  

• Version 1.0: 2011-06-08
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2020-04-15
  Changes: Data collection, Database references