Hsp90a NTD covalently bound to sulfonyl fluoride 5 at K58

Experimental Data Snapshot

  • Resolution: 1.75 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 

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Ligand Conformational Bias Drives Enantioselective Modification of a Surface-Exposed Lysine on Hsp90.

Cuesta, A.Wan, X.Burlingame, A.L.Taunton, J.

(2020) J Am Chem Soc 142: 3392-3400

  • DOI: https://doi.org/10.1021/jacs.9b09684
  • Primary Citation of Related Structures:  
    6U98, 6U99, 6U9A, 6U9B

  • PubMed Abstract: 

    Targeted covalent modification of surface-exposed lysines is challenging due to their low intrinsic reactivity and high prevalence throughout the proteome. Strategies for optimizing the rate of covalent bond formation by a reversibly bound inhibitor ( k inact ) typically involve increasing the reactivity of the electrophile, which increases the risk of off-target modification. Here, we employ an alternative approach for increasing k inact of a lysine-targeted covalent Hsp90 inhibitor, independent of the reversible binding affinity ( K i ) or the intrinsic electrophilicity. Starting with a noncovalent ligand, we appended a chiral, conformationally constrained linker, which orients an arylsulfonyl fluoride to react rapidly and enantioselectively with Lys58 on the surface of Hsp90. Biochemical experiments and high-resolution crystal structures of covalent and noncovalent ligand/Hsp90 complexes provide mechanistic insights into the role of ligand conformation in the observed enantioselectivity. Finally, we demonstrate selective covalent targeting of cellular Hsp90, which results in a prolonged heat shock response despite concomitant degradation of the covalent ligand/Hsp90 complex. Our work highlights the potential of engineering ligand conformational constraints to dramatically accelerate covalent modification of a distal, poorly nucleophilic lysine on the surface of a protein target.

  • Organizational Affiliation

    Department of Cellular and Molecular Pharmacology , University of California , San Francisco , California 94158 , United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Heat shock protein HSP 90-alpha255Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P07900 (Homo sapiens)
Explore P07900 
Go to UniProtKB:  P07900
PHAROS:  P07900
GTEx:  ENSG00000080824 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07900
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Q2A (Subject of Investigation/LOI)
Query on Q2A

Download Ideal Coordinates CCD File 
B [auth A]3-{[(3S)-3-({6-amino-8-[(6-iodo-2H-1,3-benzodioxol-5-yl)sulfanyl]-9H-purin-9-yl}methyl)piperidin-1-yl]methyl}benzene-1-sulfonyl fluoride
C25 H24 F I N6 O4 S2
Experimental Data & Validation

Experimental Data

  • Resolution: 1.75 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.564α = 90
b = 92.305β = 90
c = 99.323γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesF31CA214028

Revision History  (Full details and data files)

  • Version 1.0: 2020-02-19
    Type: Initial release
  • Version 1.1: 2020-03-04
    Changes: Database references
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Refinement description