3EKR

Dihydroxylphenyl amides as inhibitors of the Hsp90 molecular chaperone

• PDB DOI: https://doi.org/10.2210/pdb3EKR/pdb

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


• Deposited: 2008-09-19 Released: 2008-11-25 
• Deposition Author(s): Gajiwala, K.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.223 
• R-Value Work: 0.187 
• R-Value Observed: 0.189 

Starting Model: experimental

Literature

Dihydroxylphenyl amides as inhibitors of the Hsp90 molecular chaperone.

Kung, P.P., Funk, L., Meng, J., Collins, M., Zhou, J.Z., Johnson, M.C., Ekker, A., Wang, J., Mehta, P., Yin, M.J., Rodgers, C., Davies, J.F., Bayman, E., Smeal, T., Maegley, K.A., Gehring, M.R.

(2008) Bioorg Med Chem Lett 18: 6273-6278

• PubMed: 18929486 
• DOI: https://doi.org/10.1016/j.bmcl.2008.09.081
• Primary Citation of Related Structures:  
  3EKO, 3EKR


• PubMed Abstract: 
  

  Information from X-ray crystal structures were used to optimize the potency of a HTS hit in a Hsp90 competitive binding assay. A class of novel and potent small molecule Hsp90 inhibitors were thereby identified. Enantio-pure compounds 31 and 33 were potent in PGA-based competitive binding assay and inhibited proliferation of various human cancer cell lines in vitro, with IC(50) values averaging 20 nM.

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Organizational Affiliation: 

Pfizer Global Research and Development, La Jolla Laboratories, 10770, Science Center Dr., San Diego, CA 92121, USA. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 51.86 kDa 
• Atom Count: 3,747 
• Modelled Residue Count: 435 
• Deposited Residue Count: 452 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Heat shock protein HSP 90-alpha	A, B	226	Homo sapiens	Mutation(s): 0  Gene Names: HSP90AA1, HSP90A, HSPC1, HSPCA 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PY9	C [auth A], E [auth B]	4-{[(2R)-2-(2-methylphenyl)pyrrolidin-1-yl]carbonyl}benzene-1,3-diol C18 H19 N O3 TWODFUZHWYZBHZ-MRXNPFEDSA-N
PO4	D [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Binding Affinity Annotations
ID	Source	Binding Affinity
PY9	PDBBind:  3EKR	Ki: 30 (nM) from 1 assay(s)
	BindingDB:  3EKR	IC50: min: 4000, max: 9300 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.223 
• R-Value Work: 0.187 
• R-Value Observed: 0.189 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.735	α = 90
b = 79.511	β = 90
c = 118.013	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
CNX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
CNX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-11-25 
Deposition Author(s): Gajiwala, K.S.

Revision History  

• Version 1.0: 2008-11-25
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description