5AYF | pdb_00005ayf

Crystal structure of SET7/9 in complex with cyproheptadine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.258 (Depositor), 0.252 (DCC) 
  • R-Value Work: 
    0.194 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 
    0.197 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history

Literature

Identification of Cyproheptadine as an Inhibitor of SET Domain Containing Lysine Methyltransferase 7/9 (Set7/9) That Regulates Estrogen-Dependent Transcription

Takemoto, Y.Ito, A.Niwa, H.Okamura, M.Fujiwara, T.Hirano, T.Handa, N.Umehara, T.Sonoda, T.Ogawa, K.Tariq, M.Nishino, N.Dan, S.Kagechika, H.Yamori, T.Yokoyama, S.Yoshida, M.

(2016) J Med Chem 59: 3650-3660

  • DOI: https://doi.org/10.1021/acs.jmedchem.5b01732
  • Primary Citation Related Structures: 
    5AYF

  • PubMed Abstract: 

    SET domain containing lysine methyltransferase 7/9 (Set7/9), a histone lysine methyltransferase (HMT), also methylates non-histone proteins including estrogen receptor (ER) α. ERα methylation by Set7/9 stabilizes ERα and activates its transcriptional activities, which are involved in the carcinogenesis of breast cancer. We identified cyproheptadine, a clinically approved antiallergy drug, as a Set7/9 inhibitor in a high-throughput screen using a fluorogenic substrate-based HMT assay. Kinetic and X-ray crystallographic analyses revealed that cyproheptadine binds in the substrate-binding pocket of Set7/9 and inhibits its enzymatic activity by competing with the methyl group acceptor. Treatment of human breast cancer cells (MCF7 cells) with cyproheptadine decreased the expression and transcriptional activity of ERα, thereby inhibiting estrogen-dependent cell growth. Our findings suggest that cyproheptadine can be repurposed for breast cancer treatment or used as a starting point for the discovery of an anti-hormone breast cancer drug through lead optimization.


  • Organizational Affiliation
    • Chemical Genetics Laboratory, RIKEN , 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.

Macromolecule Content 

  • Total Structure Weight: 29.67 kDa 
  • Atom Count: 2,135 
  • Modeled Residue Count: 244 
  • Deposited Residue Count: 263 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Histone-lysine N-methyltransferase SETD7263Homo sapiensMutation(s): 0 
Gene Names: SETD7KIAA1717KMT7SET7SET9
EC: 2.1.1.43 (PDB Primary Data), 2.1.1.364 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q8WTS6 (Homo sapiens)
Explore Q8WTS6 
Go to UniProtKB:  Q8WTS6
PHAROS:  Q8WTS6
GTEx:  ENSG00000145391 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8WTS6
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SAM

Query on SAM



Download:Ideal Coordinates CCD File
B [auth A]S-ADENOSYLMETHIONINE
C15 H22 N6 O5 S
MEFKEPWMEQBLKI-FCKMPRQPSA-N
C7H

Query on C7H



Download:Ideal Coordinates CCD File
C [auth A]4-(dibenzo[1,2-a:2',1'-d][7]annulen-11-ylidene)-1-methyl-piperidine
C21 H21 N
JJCFRYNCJDLXIK-UHFFFAOYSA-N
TRS

Query on TRS



Download:Ideal Coordinates CCD File
D [auth A]2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.258 (Depositor), 0.252 (DCC) 
  • R-Value Work:  0.194 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 0.197 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.463α = 90
b = 39.366β = 90
c = 67.275γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data processing
PHASERphasing
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan--

Revision History  (Full details and data files)

  • Version 1.0: 2016-04-27
    Type: Initial release
  • Version 1.1: 2016-05-18
    Changes: Database references
  • Version 1.2: 2020-02-26
    Changes: Data collection, Database references, Derived calculations
  • Version 1.3: 2023-11-08
    Changes: Data collection, Database references, Refinement description
  • Version 1.4: 2024-10-23
    Changes: Structure summary