5UC4

Hsp90b N-terminal domain with inhibitors


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.167 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 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 Urologic Oncology, University of Kansas Medical Center, 3901 Rainbow Boulevard, Kansas City, KS, 66160, 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
GTEx:  ENSG00000096384 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP08238
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
83S
Query on 83S

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B],
J [auth C],
M [auth D]
5-Hydroxy-4-(isoindoline-2-carbonyl)-2-isopropylbenzaldehyde
C19 H19 N O3
SVCSVCKMYMUSOV-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
F [auth A],
K [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
DMS
Query on DMS

Download Ideal Coordinates CCD File 
G [auth A],
I [auth B],
L [auth C],
N [auth D]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
83S Binding MOAD:  5UC4 Kd: 350 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.167 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 129.251α = 90
b = 129.251β = 90
c = 106.724γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-01-17
    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