7N3M

Co-complex CYP46A1 with 0431 (compound 17)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 
    0.192 (Depositor), 0.200 (DCC) 
  • R-Value Work: 
    0.164 (Depositor), 0.180 (DCC) 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 05DClick on this verticalbar to view details

This is version 1.2 of the entry. See complete history


Literature

Discovery of Novel 3-Piperidinyl Pyridine Derivatives as Highly Potent and Selective Cholesterol 24-Hydroxylase (CH24H) Inhibitors.

Kajita, Y.Ikeda, S.Yoshikawa, M.Fukuda, H.Watanabe, E.Yano, J.Lane, W.Miyamoto, M.Ishii, T.Nishi, T.Koike, T.

(2022) J Med Chem 65: 3343-3358

  • DOI: https://doi.org/10.1021/acs.jmedchem.1c01898
  • Primary Citation of Related Structures:  
    7N3L, 7N3M

  • PubMed Abstract: 

    Cholesterol 24-hydroxylase (CH24H or CYP46A1) is a brain-specific cytochrome P450 enzyme that metabolizes cholesterol into 24 S -hydroxycholesterol (24HC) for regulating brain cholesterol homeostasis. For the development of a novel and potent CH24H inhibitor, we designed and synthesized 3,4-disubstituted pyridine derivatives using a structure-based drug design approach starting from compounds 1 (soticlestat) and 2 (thioperamide). Optimization of this series by focusing on ligand-lipophilicity efficiency value resulted in the discovery of 4-(4-methyl-1-pyrazolyl)pyridine derivative 17 (IC 50 = 8.5 nM) as a potent and highly selective CH24H inhibitor. The X-ray crystal structure of CH24H in complex with compound 17 revealed a unique binding mode. Both blood-brain barrier penetration and reduction of 24HC levels (26% reduction) in the mouse brain were confirmed by oral administration of 17 at 30 mg/kg, indicating that 17 is a promising tool for the novel and selective inhibition of CH24H.


  • Organizational Affiliation

    Research, Takeda Pharmaceutical Company Ltd, 26-1, Muraokahigashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cholesterol 24-hydroxylaseA [auth AAA]474Homo sapiensMutation(s): 0 
Gene Names: CYP46A1CYP46
EC: 1.14.14.25
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y6A2 (Homo sapiens)
Explore Q9Y6A2 
Go to UniProtKB:  Q9Y6A2
PHAROS:  Q9Y6A2
GTEx:  ENSG00000036530 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y6A2
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
B [auth AAA]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
05D (Subject of Investigation/LOI)
Query on 05D

Download Ideal Coordinates CCD File 
C [auth AAA]N,N-dimethyl-1-[4-(4-methyl-1H-pyrazol-1-yl)pyridin-3-yl]piperidine-4-carboxamide
C17 H23 N5 O
MYSVNUHQXQZBQE-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
05D BindingDB:  7N3M IC50: 8.5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free:  0.192 (Depositor), 0.200 (DCC) 
  • R-Value Work:  0.164 (Depositor), 0.180 (DCC) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.572α = 90
b = 63.717β = 90
c = 125.061γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing

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 05DClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2022-02-23
    Type: Initial release
  • Version 1.1: 2022-03-16
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Refinement description