3OWD | pdb_00003owd

Crystal Structure of HSP90 with N-Aryl-benzimidazolone II

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.63 Å
  • R-Value Free: 
    0.199 (Depositor), 0.190 (DCC) 
  • R-Value Work: 
    0.165 (Depositor), 0.160 (DCC) 
  • R-Value Observed: 
    0.167 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted MEYClick on this verticalbar to view details

This is version 1.1 of the entry. See complete history. 


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

  • 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.

    • Organizational Affiliation: 

    Cancer Research, Global Pharmaceutical R&D, Abbott Laboratories, Abbott Park, IL 60064-6101, USA. milan.bruncko@abbott.com


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Heat shock protein HSP 90-alpha207Homo sapiensMutation(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 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07900
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MEY
Query on MEY
Download Ideal Coordinates CCD File 
B [auth A]N-{[1-(5-chloro-2,4-dihydroxyphenyl)-2-oxo-2,3-dihydro-1H-benzimidazol-5-yl]methyl}naphthalene-1-sulfonamide
C24 H18 Cl N3 O5 S
VUQDPFXQYOUHGL-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
MEY BindingDB:  3OWD IC50: min: 30, max: 550 (nM) from 2 assay(s)
EC50: min: 60, max: 190 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.63 Å
  • R-Value Free:  0.199 (Depositor), 0.190 (DCC) 
  • R-Value Work:  0.165 (Depositor), 0.160 (DCC) 
  • R-Value Observed: 0.167 (Depositor) 
Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.943α = 90
b = 85.574β = 90
c = 96.844γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted MEYClick on this verticalbar to view details

View more in-depth experimental data
Entry History 

Deposition Data

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

Revision History  (Full details and data files)

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