8WTR

HUMAN SQUALENE SYNTHASE IN COMPLEX WITH (1S,3R)-3-[2-Chloro-5-(2,2-dimethyl-propyl)-13-(2-methoxy-phenyl)-6,8-dioxo-5,6,7,8,10,11-hexahydro-13H-12-oxa-5,9-diaza-benzocycloundecen-9-yl]-cyclohexanecarboxylic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.166 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Discovery of Novel 11-Membered Templates as Squalene Synthase Inhibitors.

Haginoya, N.Suzuki, M.Suzuki, M.Ishigai, Y.Terayama, K.Kanda, A.Sugita, K.

(2024) J Med Chem 67: 5305-5314

  • DOI: https://doi.org/10.1021/acs.jmedchem.3c01500
  • Primary Citation of Related Structures:  
    8WTQ, 8WTR

  • PubMed Abstract: 

    Squalene synthase is one of the most promising pharmaceutical targets to treat hyperlipidemia. Inhibition of the squalene synthase causes a decrease in the hepatic cholesterol concentration. We have already reported the design and synthesis of highly potent benzhydrol-type squalene inhibitors. Although these templates showed unique and potent cyclic active conformations via intramolecular hydrogen bonds, the in vivo cholesterol-lowering efficacy was insufficient. We attempted to improve their potential as an orally active medicine. In our medicinal chemistry effort, cyclized 11-membered ring templates were acquired. The novel series of compounds exhibited potent squalene synthase inhibitory activity, and one of the derivatives, isomer A -( 1 S , 3 R )- 14i , showed plasma lipid-lowering efficacy in hamster and marmoset repeated-dose studies. Our findings provide valuable insights into the design and development of novel and unique 11-membered ring-type highly potent squalene synthase inhibitors.


  • Organizational Affiliation

    Daiichi Sankyo RD Novare Co., Ltd., 1-16-13 Kita-Kasai, Edogawa-ku, 134-8630 Tokyo, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Squalene synthase340Homo sapiensMutation(s): 0 
Gene Names: FDFT1
EC: 2.5.1.21
UniProt & NIH Common Fund Data Resources
Find proteins for P37268 (Homo sapiens)
Explore P37268 
Go to UniProtKB:  P37268
GTEx:  ENSG00000079459 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP37268
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
KV3 (Subject of Investigation/LOI)
Query on KV3

Download Ideal Coordinates CCD File 
C [auth A](1~{S},3~{R})-3-[(10~{S})-13-chloranyl-2-(2,2-dimethylpropyl)-10-(2-methoxyphenyl)-3,5-bis(oxidanylidene)-9-oxa-2,6-diazabicyclo[9.4.0]pentadeca-1(15),11,13-trien-6-yl]cyclohexane-1-carboxylic acid
C31 H39 Cl N2 O6
CJHFRTFWDPUFCC-APLXEUBXSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
B [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.166 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.33α = 90
b = 60.016β = 116.66
c = 85.558γ = 90
Software Package:
Software NamePurpose
d*TREKdata reduction
d*TREKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-22
    Type: Initial release