8WTQ | pdb_00008wtq

HUMAN SQUALENE SYNTHASE IN COMPLEX WITH {1-[2-Chloro-5-(2,2-dimethyl-propyl)-13-(2-methoxy-phenyl)-6-oxo-6,7,10,11-tetrahydro-5H,9H,13H-12-oxa-5,8-diaza-benzocycloundecene-8-carbonyl]-piperidin-4-yl}-acetic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.206 (Depositor), 0.207 (DCC) 
  • R-Value Work: 
    0.157 (Depositor), 0.157 (DCC) 
  • R-Value Observed: 
    0.159 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 8WTQ

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 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.

Macromolecule Content 

  • Total Structure Weight: 39.86 kDa 
  • Atom Count: 3,037 
  • Modeled Residue Count: 335 
  • Deposited Residue Count: 340 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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
PHAROS:  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
KUO
(Subject of Investigation/LOI)

Query on KUO



Download:Ideal Coordinates CCD File
C [auth A]2-[1-[[(10~{S})-13-chloranyl-2-(2,2-dimethylpropyl)-10-(2-methoxyphenyl)-3-oxidanylidene-9-oxa-2,5-diazabicyclo[9.4.0]pentadeca-1(15),11,13-trien-5-yl]carbonyl]piperidin-4-yl]ethanoic acid
C32 H42 Cl N3 O6
LXTOPZNQSVXGNW-SSEXGKCCSA-N
PO4

Query on PO4



Download:Ideal Coordinates CCD File
B [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Binding Affinity Annotations 
IDSourceBinding Affinity
KUO BindingDB:  8WTQ IC50: 4.4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.206 (Depositor), 0.207 (DCC) 
  • R-Value Work:  0.157 (Depositor), 0.157 (DCC) 
  • R-Value Observed: 0.159 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.382α = 90
b = 60.017β = 117.07
c = 86.049γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
d*TREKdata scaling
d*TREKdata reduction
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