3B28

Hsp90 alpha N-terminal domain in complex with an inhibitor CH5015765


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.164 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Lead generation of heat shock protein 90 inhibitors by a combination of fragment-based approach, virtual screening, and structure-based drug design

Miura, T.Fukami, T.A.Hasegawa, K.Ono, N.Suda, A.Shindo, H.Yoon, D.O.Kim, S.J.Na, Y.J.Aoki, Y.Shimma, N.Tsukuda, T.Shiratori, Y.

(2011) Bioorg Med Chem Lett 21: 5778-5783

  • DOI: 10.1016/j.bmcl.2011.08.001
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Heat shock protein 90 (Hsp90) is a molecular chaperone which regulates maturation and stabilization of its substrate proteins, known as client proteins. Many client proteins of Hsp90 are involved in tumor progression and survival and therefore Hsp90 ...

    Heat shock protein 90 (Hsp90) is a molecular chaperone which regulates maturation and stabilization of its substrate proteins, known as client proteins. Many client proteins of Hsp90 are involved in tumor progression and survival and therefore Hsp90 can be a good target for developing anticancer drugs. With the aim of efficiently identifying a new class of orally available inhibitors of the ATP binding site of this protein, we conducted fragment screening and virtual screening in parallel against Hsp90. This approach quickly identified 2-aminotriazine and 2-aminopyrimidine derivatives as specific ligands to Hsp90 with high ligand efficiency. In silico evaluation of the 3D X-ray Hsp90 complex structures of the identified hits allowed us to promptly design CH5015765, which showed high affinity for Hsp90 and antitumor activity in human cancer xenograft mouse models.


    Organizational Affiliation

    Kamakura Research Laboratories, Chugai Pharmaceutical Co., Ltd, 200 Kajiwara, Kamakura, Kanagawa 247-8530, Japan. miuratka@chugai-pharm.co.jp



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Heat shock protein HSP 90-alphaA, B229Homo 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 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
B2X
Query on B2X

Download CCD File 
A, B
4-(5-chloro-1H,3H-benzo[de]isochromen-6-yl)-6-(methylsulfanyl)-1,3,5-triazin-2-amine
C16 H13 Cl N4 O S
FPTCGMGLTQPTGE-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
B2XKd :  3.4000000953674316   nM  PDBBind
B2XIC50:  3000   nM  BindingDB
B2XKd:  3.4000000953674316   nM  BindingDB
B2XKd:  3.4000000953674316   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.164 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.98α = 90
b = 98.81β = 124.43
c = 64.18γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
XDSdata reduction
PHASERphasing
BUSTERrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2011-07-21 
  • Released Date: 2011-09-14 
  • Deposition Author(s): Fukami, T.A., Ono, N.

Revision History 

  • Version 1.0: 2011-09-14
    Type: Initial release
  • Version 1.1: 2013-06-19
    Changes: Database references