2BZ5 | pdb_00002bz5

Structure-based Discovery of a New Class of Hsp90 Inhibitors

• PDB DOI: https://doi.org/10.2210/pdb2BZ5/pdb

• Classification: CHAPERONE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2005-08-11 Released: 2005-10-12 
• Deposition Author(s): Barril, X., Brough, P., Drysdale, M., Hubbard, R.E., Massey, A., Surgenor, A., Wright, L.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.254 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.198 (Depositor) 

Starting Model: experimental

Literature

Structure-Based Discovery of a New Class of Hsp90 Inhibitors.

Barril, X., Brough, P., Drysdale, M., Hubbard, R.E., Massey, A., Surgenor, A., Wright, L.

(2005) Bioorg Med Chem Lett 15: 5187

• PubMed: 16202589 
• DOI: https://doi.org/10.1016/j.bmcl.2005.08.092
• Primary Citation of Related Structures:  
  2BZ5


• PubMed Abstract: 
  

  Docking-based virtual screening identified 1-(2-phenol)-2-naphthol compounds as a new class of Hsp90 inhibitors of low to sub-micromolar potency. Here we report the binding affinities and cellular activities of several members of this class. A high resolution crystal structure of the most potent compound reveals its binding mode in the ATP binding site of Hsp90, providing a rationale for the observed activity of the series and suggesting strategies for developing compounds with improved properties.

---

Organizational Affiliation: 

Vernalis (R&D) Ltd, Granta Park, Abington, Cambridge CB1 6GB, UK. [e-mail]

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 53.86 kDa 
• Atom Count: 3,871 
• Modelled Residue Count: 420 
• Deposited Residue Count: 470 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HEAT SHOCK PROTEIN HSP90-ALPHA	A, B	235	Homo sapiens	Mutation(s): 0  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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AB4	C [auth A], D [auth B]	2,5-DICHLORO-N-[4-HYDROXY-3-(2-HYDROXY-1-NAPHTHYL)PHENYL]BENZENESULFONAMIDE C22 H15 Cl2 N O4 S KDKVLAFZMJRTEA-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
AB4	BindingDB:  2BZ5	IC50: min: 700, max: 2.00e+4 (nM) from 3 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.254 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.198 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.46	α = 90
b = 88.562	β = 90
c = 98.96	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
d*TREK	data reduction
d*TREK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-10-12 
Deposition Author(s): Barril, X., Brough, P., Drysdale, M., Hubbard, R.E., Massey, A., Surgenor, A., Wright, L.

Revision History  

• Version 1.0: 2005-10-12
  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: 2018-01-31
  Changes: Source and taxonomy
• Version 1.4: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description