3K99

HSP90 N-terminal domain in complex with 4-(1,3-dihydro-2H-isoindol-2-ylcarbonyl)benzene-1,3-diol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.206 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Dihydroxyphenylisoindoline amides as orally bioavailable inhibitors of the heat shock protein 90 (hsp90) molecular chaperone.

Kung, P.P.Huang, B.Zhang, G.Zhou, J.Z.Wang, J.Digits, J.A.Skaptason, J.Yamazaki, S.Neul, D.Zientek, M.Elleraas, J.Mehta, P.Yin, M.J.Hickey, M.J.Gajiwala, K.S.Rodgers, C.Davies, J.F.Gehring, M.R.

(2010) J Med Chem 53: 499-503

  • DOI: 10.1021/jm901209q
  • Primary Citation of Related Structures:  
    3K99, 3K97, 3K98

  • PubMed Abstract: 
  • The discovery and optimization of potency and metabolic stability of a novel class of dihyroxyphenylisoindoline amides as Hsp90 inhibitors are presented. Optimization of a screening hit using structure-based design and modification of log D and chemical structural features led to the identification of a class of orally bioavailable non-quinone-containing Hsp90 inhibitors ...

    The discovery and optimization of potency and metabolic stability of a novel class of dihyroxyphenylisoindoline amides as Hsp90 inhibitors are presented. Optimization of a screening hit using structure-based design and modification of log D and chemical structural features led to the identification of a class of orally bioavailable non-quinone-containing Hsp90 inhibitors. This class is exemplified by 14 and 15, which possess improved cell potency and pharmacokinetic profiles compared with the original screening hit.


    Organizational Affiliation

    Pfizer Global Research and Development, La Jolla Laboratories, 10770 Science Center Drive, San Diego, California 92121, USA. peipei.kung@pfizer.com



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Heat shock protein HSP 90-alphaA, B, C, D232Homo sapiensMutation(s): 0 
Gene Names: HSP90AA1HSP90AHSPC1HSPCA
UniProt & NIH Common Fund Data Resources
Find proteins for P07900 (Homo sapiens)
Explore P07900 
Go to UniProtKB:  P07900
PHAROS:  P07900
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PFT (Subject of Investigation/LOI)
Query on PFT

Download Ideal Coordinates CCD File 
E [auth A], F [auth B], G [auth C], H [auth D]4-(1,3-dihydro-2H-isoindol-2-ylcarbonyl)benzene-1,3-diol
C15 H13 N O3
FYANAIGOGAIFAF-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
PFT PDBBind:  3K99 Ki: 60 (nM) from 1 assay(s)
Binding MOAD:  3K99 Ki: 60 (nM) from 1 assay(s)
BindingDB:  3K99 Kd: 27.3 (nM) from 1 assay(s)
IC50: 7000 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.206 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.773α = 90
b = 82.958β = 90
c = 219.325γ = 90
Software Package:
Software NamePurpose
MAR345dtbdata collection
CNXrefinement
HKL-2000data reduction
SCALEPACKdata scaling
CNXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-02-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance