3OWD

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 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.167 

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Ligand Structure Quality Assessment 


This is version 1.0 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: 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 ...

    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
MoleculeChainsSequence LengthOrganismDetailsImage
Heat shock protein HSP 90-alphaA207Homo sapiensMutation(s): 0 
Gene Names: HSP90AA1HSP90AHSPC1HSPCA
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MEY (Subject of Investigation/LOI)
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
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
MEY BindingDB:  3OWD IC50: min: 30, max: 550 (nM) from 3 assay(s)
EC50: min: 60, max: 190 (nM) from 2 assay(s)
PDBBind:  3OWD IC50: 30 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.63 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.167 
  • 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  



Entry History 

Deposition Data

  • Deposited Date: 2010-09-17 
  • 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