2YKE

Tricyclic series of Hsp90 inhibitors


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.43 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.169 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


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

  • DOI: 10.1021/jm200784m
  • Primary Citation of Related Structures:  
    2YKB, 2YKC, 2YJW, 2YJX, 2YK9, 2YK2, 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 ...

    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.


    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HEAT SHOCK PROTEIN HSP 90-ALPHAA209Homo sapiensMutation(s): 0 
Gene Names: HSP90AA1HSP90AHSPC1HSPCA
Find proteins for P07900 (Homo sapiens)
Explore P07900 
Go to UniProtKB:  P07900
NIH Common Fund Data Resources
PHAROS  P07900
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
YKE
Query on YKE

Download CCD File 
A
N-[(4R)-4-(3H-imidazo[4,5-c]pyridin-2-yl)-4H-fluoren-9-yl]quinoline-5-carboxamide
C29 H19 N5 O
YDMHGGAKCRWQBD-JOCHJYFZSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
YKEIC50 :  1100   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.43 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.169 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.44α = 90
b = 90.87β = 90
c = 98.82γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
AMoREphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2011-05-26 
  • Released Date: 2011-10-19 
  • Deposition Author(s): Dupuy, A., Vallee, F.

Revision History 

  • Version 1.0: 2011-10-19
    Type: Initial release
  • Version 1.1: 2011-11-02
    Changes: Database references
  • Version 1.2: 2017-04-19
    Changes: Data collection