3B24

Hsp90 alpha N-terminal domain in complex with an aminotriazine fragment molecule


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.161 

wwPDB Validation 3D Report Full Report


This is version 1.2 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
  • Primary Citation of Related Structures:  

  • 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-alpha
A, B
229Homo sapiensMutation(s): 0 
Gene Names: HSP90AA1 (HSP90A, HSPC1, HSPCA)
Find proteins for P07900 (Homo sapiens)
Go to Gene View: HSP90AA1
Go to UniProtKB:  P07900
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
B2J
Query on B2J

Download SDF File 
Download CCD File 
A, B
4-(ethylsulfanyl)-6-methyl-1,3,5-triazin-2-amine
C6 H10 N4 S
PJQMCVIFTDRXNT-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
B2JKd: 42000 nM (100) BINDINGDB
B2JKd: 42000 nM BINDINGMOAD
B2JKd: 42000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.161 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 64.193α = 90.00
b = 88.510β = 90.00
c = 98.523γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
HKL-2000data reduction
TNTrefinement
HKL-2000data scaling
SCALEPACKdata scaling
BUSTERrefinement
ADSCdata collection
DENZOdata reduction
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



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
    Type: Database references
  • Version 1.2: 2017-10-11
    Type: Refinement description