5GGZ

Crystal structure of novel inhibitor bound with Hsp90


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.015 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.207 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Novel Tetrahydropyrido[4,3-d]pyrimidines as Potent Inhibitors of Chaperone Heat Shock Protein 90

Jiang, F.Wang, H.J.Jin, Y.H.Zhang, Q.Wang, Z.H.Jia, J.M.Liu, F.Wang, L.Bao, Q.C.Li, D.D.You, Q.D.Xu, X.L.

(2016) J. Med. Chem. 59: 10498-10519

  • DOI: 10.1021/acs.jmedchem.6b00912

  • PubMed Abstract: 
  • Heat shock protein 90 (Hsp90) is a potential target for oncology therapeutics. Some inhibitors have shown antitumor effects in clinical trials, spurring the discovery of small molecule Hsp90 inhibitors. Here, we describe the structural optimization s ...

    Heat shock protein 90 (Hsp90) is a potential target for oncology therapeutics. Some inhibitors have shown antitumor effects in clinical trials, spurring the discovery of small molecule Hsp90 inhibitors. Here, we describe the structural optimization studies of a hit compound, tetrahydropyrido[4,3-d]pyrimidine-based Hsp90 inhibitor 15, which exhibits inhibitory activity against Hsp90. A series of analogues were synthesized, and their structure-activity and structure-property relationships were analyzed. These explorations led to the discovery of compound 73, which exhibited potent in vitro activities, good physicochemical properties, favorable ADME properties, and a potent antitumor effect in an HCT116 xenograft model. Furthermore, 73 exhibited no ocular toxicity in a rat retinal damage model, suggesting it is a relatively safe Hsp90 inhibitor. As a promising antitumor agent, 73 was progressed for further preclinical evaluation.


    Organizational Affiliation

    State Key Laboratory of Natural Medicines and Jiang Su Key Laboratory of Drug Design and Optimization and ‡Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University , Nanjing 210009, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Heat shock protein HSP 90-alpha
B, A, D, C
210Homo 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
6TN
Query on 6TN

Download SDF File 
Download CCD File 
A, B, C, D
[2,4-bis(oxidanyl)-5-propan-2-yl-phenyl]-(2-ethoxy-7,8-dihydro-5~{H}-pyrido[4,3-d]pyrimidin-6-yl)methanone
C19 H23 N3 O4
BNTRGXQGSZZFCB-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
6TNIC50: 56 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.015 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.207 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 66.841α = 90.00
b = 88.581β = 90.08
c = 99.382γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
PHASERphasing
HKL-2000data scaling
HKL-2000data reduction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-03-08
    Type: Initial release