7K9V

Cryptococcus neoformans Hsp90 nucleotide binding domain in complex with BUCMD00452


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.165 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Fungal-Selective Resorcylate Aminopyrazole Hsp90 Inhibitors: Optimization of Whole-Cell Anticryptococcal Activity and Insights into the Structural Origins of Cryptococcal Selectivity.

Marcyk, P.T.LeBlanc, E.V.Kuntz, D.A.Xue, A.Ortiz, F.Trilles, R.Bengtson, S.Kenney, T.M.G.Huang, D.S.Robbins, N.Williams, N.S.Krysan, D.J.Prive, G.G.Whitesell, L.Cowen, L.E.Brown, L.E.

(2021) J Med Chem 64: 1139-1169

  • DOI: https://doi.org/10.1021/acs.jmedchem.0c01777
  • Primary Citation of Related Structures:  
    7K9R, 7K9S, 7K9U, 7K9V, 7K9W

  • PubMed Abstract: 

    The essential eukaryotic chaperone Hsp90 regulates the form and function of diverse client proteins, many of which govern thermotolerance, virulence, and drug resistance in fungal species. However, use of Hsp90 inhibitors as antifungal therapeutics has been precluded by human host toxicities and suppression of immune responses. We recently described resorcylate aminopyrazoles (RAPs) as the first class of Hsp90 inhibitors capable of discriminating between fungal ( Cryptococcus neoformans , Candida albicans ) and human isoforms of Hsp90 in biochemical assays. Here, we report an iterative structure-property optimization toward RAPs capable of inhibiting C. neoformans growth in culture. In addition, we report the first X-ray crystal structures of C. neoformans Hsp90 nucleotide binding domain (NBD), as the apoprotein and in complexes with the non-species-selective Hsp90 inhibitor NVP-AUY922 and three RAPs revealing unique ligand-induced conformational rearrangements, which reaffirm the hypothesis that intrinsic differences in protein flexibility can confer selective inhibition of fungal versus human Hsp90 isoforms.


  • Organizational Affiliation

    Department of Chemistry and Center for Molecular Discovery (BU-CMD), Boston University, Boston, Massachusetts 02215, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hsp90-like protein
A, B
219Cryptococcus neoformansMutation(s): 0 
UniProt
Find proteins for J9VVA4 (Cryptococcus neoformans var. grubii serotype A (strain H99 / ATCC 208821 / CBS 10515 / FGSC 9487))
Explore J9VVA4 
Go to UniProtKB:  J9VVA4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupJ9VVA4
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
W8V (Subject of Investigation/LOI)
Query on W8V

Download Ideal Coordinates CCD File 
C [auth A],
G [auth B]
(1,3-dihydro-2H-isoindol-2-yl)(2,4-dihydroxy-6-{[1-methyl-3-(2-methylphenyl)-1H-pyrazol-5-yl]amino}phenyl)methanone
C26 H24 N4 O3
XDFDFUJTCOCLHM-UHFFFAOYSA-N
BEN
Query on BEN

Download Ideal Coordinates CCD File 
D [auth A],
H [auth B]
BENZAMIDINE
C7 H8 N2
PXXJHWLDUBFPOL-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
E [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
F [auth A],
I [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.165 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 145.562α = 90
b = 44.289β = 104.355
c = 78γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01AI120958

Revision History  (Full details and data files)

  • Version 1.0: 2021-01-27
    Type: Initial release
  • Version 1.1: 2021-02-10
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Database references, Refinement description