5GGZ

Crystal structure of novel inhibitor bound with Hsp90


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.02 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.209 

wwPDB Validation 3D Report Full Report



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
  • Primary Citation of Related Structures:  
    5GGZ

  • 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Heat shock protein HSP 90-alphaA, B, C, D210Homo 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 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
6TN
Query on 6TN

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  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.02 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.209 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.841α = 90
b = 88.581β = 90.08
c = 99.382γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

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