2VW5

Structure Of The Hsp90 Inhibitor 7-O-carbamoylpremacbecin Bound To The N- Terminus Of Yeast Hsp90

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.190 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history. 


Literature

Optimizing Natural Products by Biosynthetic Engineering: Discovery of Nonquinone Hsp90 Inhibitors.

Zhang, M.Q., Gaisser, S., Nur-E-Alam, M., Sheehan, L.S., Vousden, W.A., Gaitatzis, N., Peck, G., Coates, N.J., Moss, S.J., Radzom, M., Foster, T.A., Sheridan, R.M., Gregory, M.A., Roe, S.M., Prodromou, C., Pearl, L.H., Boyd, S.M., Wilkinson, B., Martin, C.J.

(2008) J Med Chem 51: 5494

  • DOI: https://doi.org/10.1021/jm8006068
  • Primary Citation of Related Structures:  
    2VW5

  • PubMed Abstract: 

    A biosynthetic medicinal chemistry approach was applied to the optimization of the natural product Hsp90 inhibitor macbecin. By genetic engineering, mutants have been created to produce novel macbecin analogues including a nonquinone compound (5) that has significantly improved binding affinity to Hsp90 (Kd 3 nM vs 240 nM for macbecin) and reduced toxicity (MTD > or = 250 mg/kg). Structural flexibility may contribute to the preorganization of 5 to exist in solution in the Hsp90-bound conformation.

    • Organizational Affiliation: 

    Biotica Technology Limited, Chesterford Research Park, Nr. Saffron Walden, Essex CB10 1XL, United Kingdom.


Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ATP-DEPENDENT MOLECULAR CHAPERONE HSP82
A, B, C, D
214Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P02829 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P02829 
Go to UniProtKB:  P02829
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02829
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BC6
Query on BC6
Download Ideal Coordinates CCD File 
E [auth A],
I [auth B],
L [auth C],
O [auth D]		(4E,8S,9R,10E,12S,13R,14S,16R)-13,20-dihydroxy-14-methoxy-4,8,10,12,16-pentamethyl-3-oxo-2-azabicyclo[16.3.1]docosa-1(22),4,10,18,20-pentaen-9-yl carbamate
C28 H42 N2 O6
RMHMHRXSAMJROO-HZZPTFRUSA-N
SO4
Query on SO4
Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
H [auth A]
J [auth B]
K [auth B]
F [auth A],
G [auth A],
H [auth A],
J [auth B],
K [auth B],
M [auth C],
N [auth C],
P [auth D],
Q [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Binding Affinity Annotations 
IDSourceBinding Affinity
BC6 PDBBind:  2VW5 Kd: 3 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.190 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.193α = 90
b = 104.785β = 89.98
c = 109.913γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-09-02
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description