Biological Assembly 1  

 3D View: Structure | Electron Density | Validation Report | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 23.66 kDa 
• Atom Count: 1965 
• Modelled Residue Count: 207 
• Deposited Residue Count: 209 
• Unique protein chains: 1

2YK9

Tricyclic series of Hsp90 inhibitors

• DOI: 10.2210/pdb2YK9/pdb

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


• Deposited: 2011-05-26 Released: 2011-10-26 
• Deposition Author(s): Dupuy, A., Vallee, F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.32 Å
• R-Value Free: 0.195 
• R-Value Work: 0.185 
• R-Value Observed: 0.186 

Literature

Tricyclic Series of Heat Shock Protein 90 (Hsp90) Inhibitors Part I: Discovery of Tricyclic Imidazo[4,5-C]Pyridines as Potent Inhibitors of the Hsp90 Molecular Chaperone.

Vallee, F., Carrez, C., Pilorge, F., Dupuy, A., Parent, A., Bertin, L., Thompson, F., Ferrari, P., Fassy, F., Lamberton, A., Thomas, A., Arrebola, R., Guerif, S., Rohaut, A., Certal, V., Ruxer, J.M., Delorme, C., Jouanen, A., Dumas, J., Grepin, C., Combeau, C., Goulaouic, H., Dereu, N., Mikol, V., Mailliet, P., Minoux, H.

(2011) J Med Chem 54: 7206

• PubMed: 21972823 
• DOI: 10.1021/jm200784m
• Primary Citation of Related Structures:  
  2YJW, 2YJX, 2YK2, 2YK9, 2YKB, 2YKC, 2YKE, 2YKI, 2YKJ


• PubMed Abstract: 
  

A novel class of heat shock protein 90 (Hsp90) inhibitors was developed after a low throughput screen (LTS) of a focused library containing approximately 21K compounds selected by virtual screening. The initial [1-{3-H-imidazo[4-5-c]pyridin-2-yl}-3,4-dihydro-2H-pyrido[2,1-a]isoindole-6-one] (1) compound showed moderate activity (IC(50) = 7.6 μM on Hsp82, the yeast homologue of Hsp90). A high-resolution X-ray structure shows that compound 1 binds into an "induced" hydrophobic pocket, 10-15 Å away from the ATP/resorcinol binding site. Iterative cycles of structure-based drug design (SBDD) and chemical synthesis led to the design and preparation of analogues with improved affinity. These optimized molecules make productive interactions within the ATP binding site as reported by other Hsp90 inhibitors. This resulted in compound 8, which is a highly potent inhibitor in biochemical and cellular assays (K(d) = 0.35 nM on Hsp90; IC(50) = 30 nM on SKBr3 mammary carcinoma cells) and in an in vivo leukemia model.

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Organizational Affiliation: 

Sanofi-Aventis Research and Development, 13 Quai Jules Guesde, BP 14, 94400 Vitry-sur-Seine, France.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HEAT SHOCK PROTEIN HSP 90-ALPHA	A	209	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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
YK9 (Subject of Investigation/LOI)	B [auth A]	4-(1H-IMIDAZO[4,5-C]PYRIDIN-2-YL)FLUOREN-9-ONE C19 H11 N3 O MAPDUHHTXROZLC-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
YK9	PDBBind:  2YK9	IC50: 8100 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.32 Å
• R-Value Free: 0.195 
• R-Value Work: 0.185 
• R-Value Observed: 0.186 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.429	α = 90
b = 90.686	β = 90
c = 98.734	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
PROCESS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Ligand Structure Quality Assessment  

Entry History 

Deposition Data

• Deposited Date: 2011-05-26 
• Released Date: 2011-10-26 
Deposition Author(s): Dupuy, A., Vallee, F.

Revision History  

• Version 1.0: 2011-10-26
  Type: Initial release
  
• Version 1.1: 2011-11-02
  Changes: Database references