Human Hsp90 in complex with 17-desmethoxy-17-N,N-Dimethylaminoethylamino-Geldanamycin

Experimental Data Snapshot

  • Resolution: 1.75 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.184 

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This is version 1.3 of the entry. See complete history


Crystal Structure and Molecular Modeling of 17-DMAG in Complex with Human Hsp90

Jez, J.M.Chen, J.C.Rastelli, G.Stroud, R.M.Santi, D.V.

(2003) Chem Biol 10: 361-368

  • DOI: https://doi.org/10.1016/s1074-5521(03)00075-9
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Hsp90 is an attractive chemotherapeutic target because it chaperones the folding of proteins found in multiple signal transduction pathways. We describe the 1.75 A resolution crystal structure of human Hsp90 alpha (residues 9-236) complexed with 17-desmethoxy-17-N,N-dimethylaminoethylamino-geldanamycin (17-DMAG). The structure revealed an altered set of interactions between the 17-substituent and the protein compared to geldanamycin and the 17-dimethylaminoethyl moiety pointing into solvent, but otherwise was similar to that reported for the complex with geldanamycin. Targeted molecular dynamics simulations and energetic analysis indicate that geldanamycin undergoes two major conformational changes when it binds Hsp90, with the key step of the conversion being the trans to cis conformational change of the macrocycle amide bond. We speculate that 17-DMAG analogs constrained to a cis-amide in the ground state could provide a significant increase in affinity for Hsp90.

  • Organizational Affiliation

    Kosan Biosciences, Inc., 3832 Bay Center Place, Hayward, CA 94545, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
heat shock 90kDa protein 1, alpha; heat shock 90kD protein 1, alpha215Homo 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 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on KOS

Download Ideal Coordinates CCD File 
C32 H48 N4 O8
Query on MPD

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]
C6 H14 O2
Query on ACY

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A]
C2 H4 O2
Binding Affinity Annotations 
IDSourceBinding Affinity
KOS BindingDB:  1OSF IC50: min: 4.5, max: 1410 (nM) from 8 assay(s)
EC50: 7.9 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.75 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.184 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.71α = 90
b = 41.68β = 102.81
c = 55.98γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
CCP4data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-05-27
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-02-14
    Changes: Data collection, Database references, Derived calculations