3B26

Hsp90 alpha N-terminal domain in complex with an inhibitor Ro1127850

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.158 

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
  • 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 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
B2L
Query on B2L
Download SDF File 
Download CCD File 
A
4-(1H,3H-benzo[de]isochromen-6-yl)-6-methylpyrimidin-2-amine
C17 H15 N3 O
RUGFWNOTXBMCJB-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
B2LKd: 230 nM (100) BINDINGDB
B2LIC50: 6900 nM (100) BINDINGDB
B2LKd: 230 nM BINDINGMOAD
B2LKd: 230 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.158 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 64.223α = 90.00
b = 88.704β = 90.00
c = 98.840γ = 90.00
Software Package:
Software NamePurpose
BUSTERrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
MOLREPphasing
SCALEPACKdata scaling
TNTrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

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