7LT0 | pdb_00007lt0

Hsp90a N-terminal inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 
    0.204 (Depositor), 0.204 (DCC) 
  • R-Value Work: 
    0.176 (Depositor), 0.177 (DCC) 
  • R-Value Observed: 
    0.178 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history

Literature

Selective Inhibition of the Hsp90 alpha Isoform.

Mishra, S.J.Khandelwal, A.Banerjee, M.Balch, M.Peng, S.Davis, R.E.Merfeld, T.Munthali, V.Deng, J.Matts, R.L.Blagg, B.S.J.

(2021) Angew Chem Int Ed Engl 60: 10547-10551

  • DOI: https://doi.org/10.1002/anie.202015422
  • Primary Citation Related Structures: 
    7LSZ, 7LT0

  • PubMed Abstract: 

    The 90 kDa heat shock protein (Hsp90) is a molecular chaperone that processes nascent polypeptides into their biologically active conformations. Many of these proteins contribute to the progression of cancer, and consequently, inhibition of the Hsp90 protein folding machinery represents an innovative approach toward cancer chemotherapy. However, clinical trials with Hsp90 N-terminal inhibitors have encountered deleterious side effects and toxicities, which appear to result from the pan-inhibition of all four Hsp90 isoforms. Therefore, the development of isoform-selective Hsp90 inhibitors is sought to delineate the pathological role played by each isoform. Herein, we describe a structure-based approach that was used to design the first Hsp90α-selective inhibitors, which exhibit >50-fold selectivity versus other Hsp90 isoforms.


  • Organizational Affiliation
    • Department of Chemistry and Biochemistry, The University of Notre Dame, 305 McCourtney Hall, Notre Dame, IN, 46556, USA.

Macromolecule Content 

  • Total Structure Weight: 33.88 kDa 
  • Atom Count: 1,985 
  • Modeled Residue Count: 208 
  • Deposited Residue Count: 293 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Heat shock protein HSP 90-alpha293Homo sapiensMutation(s): 0 
Gene Names: HSP90AA1HSP90AHSPC1HSPCA
EC: 3.6.4.10
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
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ONJ
(Subject of Investigation/LOI)

Query on ONJ



Download:Ideal Coordinates CCD File
B [auth A](1,3-dihydro-2H-isoindol-2-yl){3-[(3,4-dimethylphenyl)sulfanyl]-4-hydroxyphenyl}methanone
C23 H21 N O2 S
AXEQZLWHIYQNKM-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
ONJ BindingDB:  7LT0 Kd: 840 (nM) from 1 assay(s)
IC50: 840 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free:  0.204 (Depositor), 0.204 (DCC) 
  • R-Value Work:  0.176 (Depositor), 0.177 (DCC) 
  • R-Value Observed: 0.178 (Depositor) 
Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.614α = 90
b = 90.119β = 90
c = 97.967γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-03-03
    Type: Initial release
  • Version 1.1: 2021-03-10
    Changes: Database references
  • Version 1.2: 2021-04-07
    Changes: Database references
  • Version 1.3: 2021-05-05
    Changes: Database references
  • Version 1.4: 2023-10-18
    Changes: Advisory, Data collection, Database references, Refinement description