3WHA

Hsp90 alpha N-terminal domain in complex with a tricyclic inhibitor

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.185 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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Literature

Design and synthesis of 2-amino-6-(1H,3H-benzo[de]isochromen-6-yl)-1,3,5-triazines as novel Hsp90 inhibitors

Suda, A., Kawasaki, K., Komiyama, S., Isshiki, Y., Yoon, D.-O., Kim, S.-J., Na, Y.-J., Hasegawa, K., Fukami, T.A., Sato, S., Miura, T., Ono, N., Yamazaki, T., Saitoh, R., Shimma, N., Shiratori, Y., Tsukuda, T.

(2014) Bioorg Med Chem 22: 892-905

  • DOI: 10.1016/j.bmc.2013.11.036
  • Primary Citation of Related Structures:  
    3WHA

  • PubMed Abstract: 

    • A novel series of 2-amino-1,3,5-triazines bearing a tricyclic moiety as heat shock protein 90 (Hsp90) inhibitors is described. Molecular design was performed using X-ray cocrystal structures of the lead compound CH5015765 and natural Hsp90 inhibitor geldanamycin with Hsp90 ...

    A novel series of 2-amino-1,3,5-triazines bearing a tricyclic moiety as heat shock protein 90 (Hsp90) inhibitors is described. Molecular design was performed using X-ray cocrystal structures of the lead compound CH5015765 and natural Hsp90 inhibitor geldanamycin with Hsp90. We optimized affinity to Hsp90, in vitro cell growth inhibitory activity, water solubility, and liver microsomal stability of inhibitors and identified CH5138303. This compound showed high binding affinity for N-terminal Hsp90α (Kd=0.52nM) and strong in vitro cell growth inhibition against human cancer cell lines (HCT116 IC50=0.098μM, NCI-N87 IC50=0.066μM) and also displayed high oral bioavailability in mice (F=44.0%) and potent antitumor efficacy in a human NCI-N87 gastric cancer xenograft model (tumor growth inhibition=136%).

    Organizational Affiliation: 

    Research Division, Chugai Pharmaceutical Co., Ltd, 200 Kajiwara, Kamakura, Kanagawa 247-8530, Japan.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Heat shock protein HSP 90-alphaA, B229Homo sapiensMutation(s): 0 
Gene Names: HSP90AA1, HSP90A, HSPC1, HSPCA
EC: 3.6.4.10
UniProt & NIH Common Fund Data Resources
Find proteins for P07900 (Homo sapiens)
Explore P07900 
Go to UniProtKB:  P07900
PHAROS:  P07900
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07900
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
WHA
Query on WHA
Download Ideal Coordinates CCD File 
D [auth A],
E [auth B]		4-{[4-amino-6-(5-chloro-1H,3H-benzo[de]isochromen-6-yl)-1,3,5-triazin-2-yl]sulfanyl}butanamide
C19 H18 Cl N5 O2 S
VIGHQZSTZWNWFA-UHFFFAOYSA-N		 Ligand Interaction
GOL
Query on GOL
Download Ideal Coordinates CCD File 
C [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
F [auth B]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
WHA Binding MOAD:  3WHA Kd: 0.48 (nM) from 1 assay(s)
BindingDB:  3WHA Kd: 0.48 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.185 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.17α = 90
b = 98.92β = 124.55
c = 64.24γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PHASERphasing
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
BUSTERrefinement

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

  • Deposited Date: 2013-08-23 
  • Released Date: 2014-01-29 
    • Deposition Author(s): Fukami, T.A., Ono, N.

Revision History  (Full details and data files)

  • Version 1.0: 2014-01-29
    Type: Initial release