3OW6

Crystal Structure of HSP90 with N-Aryl-benzimidazolone I

• PDB DOI: https://doi.org/10.2210/pdb3OW6/pdb

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


• Deposited: 2010-09-17 Released: 2011-09-21 
• Deposition Author(s): Park, C.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.220 
• R-Value Work: 0.192 
• R-Value Observed: 0.193 

Literature

N-aryl-benzimidazolones as novel small molecule HSP90 inhibitors.

Bruncko, M., Tahir, S.K., Song, X., Chen, J., Ding, H., Huth, J.R., Jin, S., Judge, R.A., Madar, D.J., Park, C.H., Park, C.M., Petros, A.M., Tse, C., Rosenberg, S.H., Elmore, S.W.

(2010) Bioorg Med Chem Lett 20: 7503-7506

• PubMed: 21106457 
• DOI: https://doi.org/10.1016/j.bmcl.2010.10.010
• Primary Citation of Related Structures:  
  3OW6, 3OWB, 3OWD


• PubMed Abstract: 
  

  We describe the development of a novel series of N-aryl-benzimidazolone HSP90 inhibitors (9) targeting the N-terminal ATP-ase site. SAR development was influenced by structure-based design based around X-ray structures of ligand bound HSP90 complexes. Lead compounds exhibited high binding affinities, ATP-ase inhibition and cellular client protein degradation.

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Organizational Affiliation: 

Cancer Research, Global Pharmaceutical R&D, Abbott Laboratories, Abbott Park, IL 60064-6101, USA. [e-mail]

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 23.39 kDa 
• Atom Count: 1,910 
• Modelled Residue Count: 207 
• Deposited Residue Count: 207 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Heat shock protein HSP 90-alpha	A	207	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
MEX	B [auth A]	1-(2,4-dihydroxyphenyl)-1,3-dihydro-2H-benzimidazol-2-one C13 H10 N2 O3 VCZFDVVMKKLXAN-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
MEX	BindingDB:  3OW6	IC50: min: 220, max: 8.50e+4 (nM) from 2 assay(s)
	PDBBind:  3OW6	IC50: 220 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.220 
• R-Value Work: 0.192 
• R-Value Observed: 0.193 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.495	α = 90
b = 89.482	β = 90
c = 88.107	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
BUSTER-TNT	refinement
PDB_EXTRACT	data extraction
ADSC	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-09-21 
Deposition Author(s): Park, C.H.

Revision History  

• Version 1.0: 2011-09-21
  Type: Initial release
  
• Version 1.1: 2024-02-21
  Changes: Data collection, Database references, Derived calculations