2BYI

3-(5-chloro-2,4-dihydroxyphenyl)-pyrazole-4-carboxamides as Inhibitors of the Hsp90 Molecular Chaperone

• PDB DOI: https://doi.org/10.2210/pdb2BYI/pdb

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


• Deposited: 2005-08-02 Released: 2005-10-12 
• Deposition Author(s): Brough, P.A., Barril, X., Beswick, M., Dymock, B.W., Drysdale, M.J., Wright, L., Grant, K., Massey, A., Surgenor, A., Workman, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.242 
• R-Value Work: 0.195 
• R-Value Observed: 0.197 

Starting Model: experimental

Literature

3-(5-Chloro-2,4-Dihydroxyphenyl)-Pyrazole-4-Carboxamides as Inhibitors of the Hsp90 Molecular Chaperone.

Brough, P.A., Barril, X., Beswick, M., Dymock, B.W., Drysdale, M.J., Wright, L., Grant, K., Massey, A., Surgenor, A., Workman, P.

(2005) Bioorg Med Chem Lett 15: 5197

• PubMed: 16213716 
• DOI: https://doi.org/10.1016/j.bmcl.2005.08.091
• Primary Citation of Related Structures:  
  2BYH, 2BYI


• PubMed Abstract: 
  

  Information from X-ray crystal structures of Hsp90 inhibitors bound to the human Hsp90 molecular chaperone was used to assist in the design of 3-(5-chloro-2,4-dihydroxyphenyl)-pyrazole-4-carboxamides as novel inhibitors of Hsp90. Accessing an extra interaction with the protein via Phe138 gave a significant increase in binding potency compared to similar analogues that do not make this interaction.

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Organizational Affiliation: 

Vernalis Ltd, Granta Park, Great 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)

Macromolecule Content

• Total Structure Weight: 26.89 kDa 
• Atom Count: 1,984 
• Modelled Residue Count: 215 
• Deposited Residue Count: 235 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HEAT SHOCK PROTEIN HSP90-ALPHA	A	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
2DD	B [auth A]	3-(5-CHLORO-2,4-DIHYDROXY-PHENYL)-1H-PYRAZOLE-4-CARBOXYLIC ACID 4-SULFAMOYL-BENZYLAMIDE C17 H15 Cl N4 O5 S OOHYJGNSESWEFT-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
2DD	PDBBind:  2BYI	IC50: 461 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.242 
• R-Value Work: 0.195 
• R-Value Observed: 0.197 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.296	α = 90
b = 44.049	β = 115.28
c = 54.176	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): Brough, P.A., Barril, X., Beswick, M., Dymock, B.W., Drysdale, M.J., Wright, L., Grant, K., Massey, A., Surgenor, A., Workman, P.

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: 2023-12-13
  Changes: Data collection, Database references, Other, Refinement description