2BSM | pdb_00002bsm

Novel, potent small molecule inhibitors of the molecular chaperone Hsp90 discovered through structure-based design

• PDB DOI: https://doi.org/10.2210/pdb2BSM/pdb

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


• Deposited: 2005-05-23 Released: 2005-06-02 
• Deposition Author(s): Dymock, B.W., Barril, X., Brough, P.A., Cansfield, J.E., Massey, A., McDonald, E., Hubbard, R.E., Surgenor, A., Roughley, S.D., Webb, P., Workman, P., Wright, L., Drysdale, M.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 
  0.244 (Depositor), 0.253 (DCC) 
• R-Value Work: 
  0.192 (Depositor), 0.204 (DCC) 
• R-Value Observed: 
  0.195 (Depositor) 

Starting Model: experimental

Literature

Novel, potent small-molecule inhibitors of the molecular chaperone Hsp90 discovered through structure-based design.

Dymock, B.W., Barril, X., Brough, P.A., Cansfield, J.E., Massey, A., McDonald, E., Hubbard, R.E., Surgenor, A., Roughley, S.D., Webb, P., Workman, P., Wright, L., Drysdale, M.J.

(2005) J Med Chem 48: 4212-4215

• PubMed: 15974572 
• DOI: https://doi.org/10.1021/jm050355z
• Primary Citation Related Structures: 
  2BSM, 2BT0


• PubMed Abstract: 
  

  The crystal structure of a previously reported screening hit 1 (CCT018159) bound to the N terminal domain of molecular chaperone Hsp90 has been used to design 5-amide analogues. These exhibit enhanced potency against the target in binding and functional assays with accompanying appropriate cellular pharmacodynamic changes. Compound 11 (VER-49009) compares favorably with the clinically evaluated 17-AAG.

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Organizational Affiliation: 
• Vernalis Ltd., Granta Park, Great Abington, Cambridge, UK.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 26.86 kDa 
• Atom Count: 1,902 
• Modeled Residue Count: 209 
• 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
BSM	B [auth A]	5-(5-CHLORO-2,4-DIHYDROXYPHENYL)-N-ETHYL-4-(4-METHOXYPHENYL)-1H-PYRAZOLE-3-CARBOXAMIDE C19 H18 Cl N3 O4 HUNAOTXNHVALTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free:  0.244 (Depositor), 0.253 (DCC) 
• R-Value Work:  0.192 (Depositor), 0.204 (DCC) 
• R-Value Observed: 0.195 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.398	α = 90
b = 88.841	β = 90
c = 99.273	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: 2005-06-02 
Deposition Author(s): Dymock, B.W., Barril, X., Brough, P.A., Cansfield, J.E., Massey, A., McDonald, E., Hubbard, R.E., Surgenor, A., Roughley, S.D., Webb, P., Workman, P., Wright, L., Drysdale, M.J.

Revision History  

• Version 1.0: 2005-06-02
  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: 2018-02-28
  Changes: Database references
• Version 1.4: 2023-12-13
  Changes: Data collection, Database references, Other, Refinement description