RCSB PDB - 3VHD: Hsp90 alpha N-terminal domain in complex with a macrocyclic inhibitor, CH5164840

 3VHD

Hsp90 alpha N-terminal domain in complex with a macrocyclic inhibitor, CH5164840


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.52 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.166 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

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This is version 1.1 of the entry. See complete history


Literature

Design and synthesis of novel macrocyclic 2-amino-6-arylpyrimidine Hsp90 inhibitors

Suda, A.Koyano, H.Hayase, T.Hada, K.Kawasaki, K.Komiyama, S.Hasegawa, K.Fukami, T.A.Sato, S.Miura, T.Ono, N.Yamazaki, T.Saitoh, R.Shimma, N.Shiratori, Y.Tsukuda, T.

(2012) Bioorg Med Chem Lett 22: 1136-1141

  • DOI: https://doi.org/10.1016/j.bmcl.2011.11.100
  • Primary Citation of Related Structures:  
    3VHA, 3VHC, 3VHD

  • PubMed Abstract: 

    Macrocyclic compounds bearing a 2-amino-6-arylpyrimidine moiety were identified as potent heat shock protein 90 (Hsp90) inhibitors by modification of 2-amino-6-aryltriazine derivative (CH5015765). We employed a macrocyclic structure as a skeleton of new inhibitors to mimic the geldanamycin-Hsp90 interactions. Among the identified inhibitors, CH5164840 showed high binding affinity for N-terminal Hsp90α (K(d)=0.52nM) and strong anti-proliferative activity against human cancer cell lines (HCT116 IC(50)=0.15μM, NCI-N87 IC(50)=0.066μM). CH5164840 displayed high oral bioavailability in mice (F=70.8%) and potent antitumor efficacy in a HCT116 human colorectal cancer xenograft model (tumor growth inhibition=83%).


  • Organizational Affiliation

    Kamakura Laboratories, Research Division, Chugai Pharmaceutical Co., Ltd, 200 Kajiwara, Kamakura, Kanagawa 247-8530, Japan. sudaats@chugai-pharm.co.jp


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Heat shock protein HSP 90-alpha
A, B
229Homo sapiensMutation(s): 0 
Gene Names: HSP90AA1
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
GTEx:  ENSG00000080824 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07900
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
VHE
Query on VHE

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
4-amino-18,20-dimethyl-7-thia-3,5,11,15-tetraazatricyclo[15.3.1.1(2,6)]docosa-1(20),2,4,6(22),17(21),18-hexaene-10,16-dione
C19 H23 N5 O2 S
OMFBVBRFVYLRQT-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
VHE BindingDB:  3VHD Kd: 0.52 (nM) from 1 assay(s)
PDBBind:  3VHD Kd: 0.52 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.52 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.166 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.995α = 114.6
b = 53.061β = 91.12
c = 54.178γ = 90.17
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction
BUSTERrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted VHEClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-07-18
    Type: Initial release
  • Version 1.1: 2024-03-20
    Changes: Data collection, Database references, Derived calculations