2VWC

STRUCTURE OF THE HSP90 INHIBITOR MACBECIN BOUND TO THE N-TERMINUS OF YEAST HSP90.

• PDB DOI: https://doi.org/10.2210/pdb2VWC/pdb
• Entry: 2VWC supersedes: 2VLS

• Classification: CHAPERONE
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-06-20 Released: 2008-07-01 
• Deposition Author(s): Roe, S.M., Prodromou, C., Pearl, L.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.262 
• R-Value Work: 0.195 
• R-Value Observed: 0.198 

Literature

Molecular Characterisation of Macbecin as an Hsp90 Inhibitor

Martin, C.J., Gaisser, S., Challis, I.R., Carletti, I., Wilkinson, B., Gregory, M., Prodromou, C., Roe, S.M., Pearl, L.H., Boyd, S.M., Zhang, M.Q.

(2008) J Med Chem 51: 2853

• PubMed: 18357975 
• DOI: https://doi.org/10.1021/jm701558c
• Primary Citation of Related Structures:  
  2VWC


• PubMed Abstract: 
  

  Macbecin compares favorably to geldanamycin as an Hsp90 inhibitor, being more soluble, stable, more potently inhibiting ATPase activity (IC50 = 2 microM) and binding with higher affinity (Kd = 0.24 microM). Structural studies reveal significant differences in their Hsp90 binding characteristics, and macbecin-induced tumor cell growth inhibition is accompanied by characteristic degradation of Hsp90 client proteins. Macbecin significantly reduced tumor growth rates (minimum T/C: 32%) in a DU145 murine xenograft. Macbecin thus represents an attractive lead for further optimization.

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Organizational Affiliation: 

Biotica Technology Limited, Chesterford Research Park, Essex CB10 1XL, U.K. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 25.43 kDa 
• Atom Count: 1,887 
• Modelled Residue Count: 214 
• Deposited Residue Count: 219 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-DEPENDENT MOLECULAR CHAPERONE HSP82	A	219	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P02829 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P02829  Go to UniProtKB:  P02829

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BC2	B [auth A]	MACBECIN C30 H42 N2 O8 PLTGBUPHJAKFMA-CISVGLRTSA-N
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
BC2	Binding MOAD:  2VWC	Kd: 240 (nM) from 1 assay(s)
	PDBBind:  2VWC	Kd: 240 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.262 
• R-Value Work: 0.195 
• R-Value Observed: 0.198 
• Space Group: P 4₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.805	α = 90
b = 73.805	β = 90
c = 110.667	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-07-01 
Deposition Author(s): Roe, S.M., Prodromou, C., Pearl, L.H.
• This entry supersedes: 2VLS

Revision History  

• Version 1.0: 2008-07-01
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2023-12-13
  Changes: Data collection, Database references, Other, Refinement description