6N8Y

Hsp90-beta bound to PU-11-trans


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.165 

wwPDB Validation   3D Report Full Report

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This is version 1.4 of the entry. See complete history


Literature

Structures of Hsp90 alpha and Hsp90 beta bound to a purine-scaffold inhibitor reveal an exploitable residue for drug selectivity.

Huck, J.D.Que, N.L.S.Sharma, S.Taldone, T.Chiosis, G.Gewirth, D.T.

(2019) Proteins 87: 869-877

  • DOI: https://doi.org/10.1002/prot.25750
  • Primary Citation of Related Structures:  
    6N8W, 6N8X, 6N8Y, 6OLX

  • PubMed Abstract: 

    Hsp90α and Hsp90β are implicated in a number of cancers and neurodegenerative disorders but the lack of selective pharmacological probes confounds efforts to identify their individual roles. Here, we analyzed the binding of an Hsp90α-selective PU compound, PU-11-trans, to the two cytosolic paralogs. We determined the co-crystal structures of Hsp90α and Hsp90β bound to PU-11-trans, as well as the structure of the apo Hsp90β NTD. The two inhibitor-bound structures reveal that Ser52, a nonconserved residue in the ATP binding pocket in Hsp90α, provides additional stability to PU-11-trans through a water-mediated hydrogen-bonding network. Mutation of Ser52 to alanine, as found in Hsp90β, alters the dissociation constant of Hsp90α for PU-11-trans to match that of Hsp90β. Our results provide a structural explanation for the binding preference of PU inhibitors for Hsp90α and demonstrate that the single nonconserved residue in the ATP-binding pocket may be exploited for α/β selectivity.


  • Organizational Affiliation

    Program in Chemical Biology and Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Heat shock protein HSP 90-beta241Homo 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 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
KFY (Subject of Investigation/LOI)
Query on KFY

Download Ideal Coordinates CCD File 
B [auth A]9-[(2E)-but-2-en-1-yl]-8-[(3,4,5-trimethoxyphenyl)methyl]-9H-purin-6-amine
C19 H23 N5 O3
ZAFMHPQRCYVTLV-AATRIKPKSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
KFY Binding MOAD:  6N8Y Kd: 4200 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.165 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.144α = 90
b = 90.959β = 90
c = 96.196γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesP01CA186866
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesR01CA095130

Revision History  (Full details and data files)

  • Version 1.0: 2019-07-03
    Type: Initial release
  • Version 1.1: 2019-07-10
    Changes: Data collection, Database references
  • Version 1.2: 2019-09-11
    Changes: Data collection, Database references
  • Version 1.3: 2019-12-04
    Changes: Author supporting evidence
  • Version 1.4: 2023-10-11
    Changes: Data collection, Database references, Refinement description