4L8Z

Crystal structure of Human Hsp90 with RL1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.703 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Identification of a new series of potent diphenol HSP90 inhibitors by fragment merging and structure-based optimization

Ren, J.Li, J.Wang, Y.Chen, W.Shen, A.Liu, H.Chen, D.Cao, D.Li, Y.Zhang, N.Xu, Y.Geng, M.He, J.Xiong, B.Shen, J.

(2014) Bioorg.Med.Chem.Lett. 24: 2525-2529

  • DOI: 10.1016/j.bmcl.2014.03.100
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Heat shock protein 90 (HSP90) is a molecular chaperone to fold and maintain the proper conformation of many signaling proteins, especially some oncogenic proteins and mutated unstable proteins. Inhibition of HSP90 was recognized as an effective appro ...

    Heat shock protein 90 (HSP90) is a molecular chaperone to fold and maintain the proper conformation of many signaling proteins, especially some oncogenic proteins and mutated unstable proteins. Inhibition of HSP90 was recognized as an effective approach to simultaneously suppress several aberrant signaling pathways, and therefore it was considered as a novel target for cancer therapy. Here, by integrating several techniques including the fragment-based drug discovery method, fragment merging, computer aided inhibitor optimization, and structure-based drug design, we were able to identify a series of HSP90 inhibitors. Among them, inhibitors 13, 32, 36 and 40 can inhibit HSP90 with IC50 about 20-40 nM, which is at least 200-fold more potent than initial fragments in the protein binding assay. These new HSP90 inhibitors not only explore interactions with an under-studied subpocket, also offer new chemotypes for the development of novel HSP90 inhibitors as anticancer drugs.


    Organizational Affiliation

    Division of Antitumor Pharmacology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China.,Department of Medicinal Chemistry, National Key Laboratory of New Drug, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China.,Shanghai Institute of Applied Physics, Chinese Academy of Sciences, 239 Zhangheng Road, Shanghai 201204, China. Electronic address: hejh@sinap.ac.cn.,Division of Antitumor Pharmacology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China. Electronic address: mygeng@simm.ac.cn.,CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China.,Department of Medicinal Chemistry, National Key Laboratory of New Drug, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China. Electronic address: bxiong@simm.ac.cn.,Shanghai Institute of Applied Physics, Chinese Academy of Sciences, 239 Zhangheng Road, Shanghai 201204, China; CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Heat shock protein HSP 90-alpha
A
228Homo 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
RL1
Query on RL1

Download SDF File 
Download CCD File 
A
[5-(6-bromo[1,2,4]triazolo[4,3-a]pyridin-3-yl)-2,4-dihydroxyphenyl](3,4-dihydroisoquinolin-2(1H)-yl)methanone
C22 H17 Br N4 O3
PQZGUYBCXAZFGQ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
RL1IC50: 18700 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.703 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.194 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 69.853α = 90.00
b = 88.565β = 90.00
c = 97.964γ = 90.00
Software Package:
Software NamePurpose
PHENIXmodel building
PHENIXrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-06-18
    Type: Initial release