3RKZ | pdb_00003rkz

Discovery of a stable macrocyclic o-aminobenzamide Hsp90 inhibitor capable of significantly decreasing tumor volume in a mouse xenograft model.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.57 Å
  • R-Value Free: 
    0.188 (Depositor), 0.190 (DCC) 
  • R-Value Work: 
    0.165 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 
    0.167 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

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This is version 1.2 of the entry. See complete history


Literature

Discovery of a stable macrocyclic o-aminobenzamide Hsp90 inhibitor which significantly decreases tumor volume in a mouse xenograft model.

Zapf, C.W.Bloom, J.D.Li, Z.Dushin, R.G.Nittoli, T.Otteng, M.Nikitenko, A.Golas, J.M.Liu, H.Lucas, J.Boschelli, F.Vogan, E.Olland, A.Johnson, M.Levin, J.I.

(2011) Bioorg Med Chem Lett 21: 4602-4607

  • DOI: https://doi.org/10.1016/j.bmcl.2011.05.102
  • Primary Citation of Related Structures:  
    3RKZ

  • PubMed Abstract: 

    An extension of our previously reported series of macrocyclic ortho-aminobenzamide Hsp90 inhibitors is reported. Addition of a second methyl group to the tether provided analogs that show increased potency in binding as well as cell-proliferation assays and, more importantly, are stable toward microsomes. We wish to disclose the discovery of a macrocycle which showed impressive biomarker activity 24-h post dosing and which demonstrated prolonged exposure in tumors. When studied in a lung cancer xenograft model, the compound demonstrated significant tumor size reduction.


  • Organizational Affiliation

    Medicinal Chemistry, Pfizer, Pearl River, NY 10965, United States. christoph.zapf@pfizer.com


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Heat shock protein HSP 90-alpha226Homo sapiensMutation(s): 0 
Gene Names: HSP90AHSP90AA1HSPC1HSPCA
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
06T
Query on 06T

Download Ideal Coordinates CCD File 
B [auth A](5R,6S)-3-(L-alanyl)-5,6,15,15,18-pentamethyl-17-oxo-2,3,4,5,6,7,14,15,16,17-decahydro-1H-12,8-(metheno)[1,5,9]triazacyclotetradecino[1,2-a]indole-9-carboxamide
C28 H39 N5 O3
JSSUIPOIXFFFQU-NJAFHUGGSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
06T BindingDB:  3RKZ IC50: 83 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.57 Å
  • R-Value Free:  0.188 (Depositor), 0.190 (DCC) 
  • R-Value Work:  0.165 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 0.167 (Depositor) 
Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.001α = 90
b = 90.178β = 90
c = 97.957γ = 90
Software Package:
Software NamePurpose
StructureStudiodata collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 06TClick on this verticalbar to view details

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2011-07-13
    Type: Initial release
  • Version 1.1: 2011-08-03
    Changes: Database references
  • Version 1.2: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description