5UCJ | pdb_00005ucj

Hsp90b N-terminal domain with inhibitors


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free: 
    0.197 (Depositor), 0.200 (DCC) 
  • R-Value Work: 
    0.174 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 
    0.175 (Depositor) 

Starting Model: experimental
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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 KU3Click on this verticalbar to view details

This is version 1.3 of the entry. See complete history


Literature

Structure-guided design of an Hsp90 beta N-terminal isoform-selective inhibitor.

Khandelwal, A.Kent, C.N.Balch, M.Peng, S.Mishra, S.J.Deng, J.Day, V.W.Liu, W.Subramanian, C.Cohen, M.Holzbeierlein, J.M.Matts, R.Blagg, B.S.J.

(2018) Nat Commun 9: 425-425

  • DOI: https://doi.org/10.1038/s41467-017-02013-1
  • Primary Citation of Related Structures:  
    5UC4, 5UCH, 5UCI, 5UCJ

  • PubMed Abstract: 

    The 90 kDa heat shock protein (Hsp90) is a molecular chaperone responsible for folding proteins that are directly associated with cancer progression. Consequently, inhibition of the Hsp90 protein folding machinery results in a combinatorial attack on numerous oncogenic pathways. Seventeen small-molecule inhibitors of Hsp90 have entered clinical trials, all of which bind the Hsp90 N-terminus and exhibit pan-inhibitory activity against all four Hsp90 isoforms. pan-Inhibition of Hsp90 appears to be detrimental as toxicities have been reported alongside induction of the pro-survival heat shock response. The development of Hsp90 isoform-selective inhibitors represents an alternative approach towards the treatment of cancer that may limit some of the detriments. Described herein is a structure-based approach to design isoform-selective inhibitors of Hsp90β, which induces the degradation of select Hsp90 clients without concomitant induction of Hsp90 levels. Together, these initial studies support the development of Hsp90β-selective inhibitors as a method to overcome the detriments associated with pan-inhibition.


  • Organizational Affiliation

    Department of Medicinal Chemistry, The University of Kansas, 1251 Wescoe Hall Drive, Malott Hall 4048, Lawrence, KS, 66045, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Heat shock protein HSP 90-beta
A, B, C, D
220Homo sapiensMutation(s): 0 
Gene Names: HSP90AB1HSP90BHSPC2HSPCB
UniProt & NIH Common Fund Data Resources
Find proteins for P08238 (Homo sapiens)
Explore P08238 
Go to UniProtKB:  P08238
PHAROS:  P08238
GTEx:  ENSG00000096384 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP08238
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
KU3
Query on KU3

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B],
K [auth C],
M [auth D]
(5-fluoroisoindolin-2-yl)(4-hydroxy-5-isopropylbenzo[d]isoxazol-7-yl)methanone
C19 H17 F N2 O3
XKVXUSFQFBIYEQ-UHFFFAOYSA-N
DMS
Query on DMS

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
I [auth B]
J [auth B]
L [auth C]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free:  0.197 (Depositor), 0.200 (DCC) 
  • R-Value Work:  0.174 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 0.175 (Depositor) 
Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 129.464α = 90
b = 129.464β = 90
c = 106.357γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing

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 KU3Click on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-01-10
    Type: Initial release
  • Version 1.1: 2018-03-07
    Changes: Database references
  • Version 1.2: 2023-10-04
    Changes: Advisory, Data collection, Database references, Refinement description
  • Version 1.3: 2024-10-23
    Changes: Structure summary