3Q30

Human Squalene synthase in complex with (2R,3R)-2-Carboxymethoxy-3-[5-(2-naphthalenyl)pentyl]aminocarbonyl-3-[5-(2-naphthalenyl)pentyloxy]propionic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.207 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Discovery of a new 2-aminobenzhydrol template for highly potent squalene synthase inhibitors

Ichikawa, M.Yokomizo, A.Itoh, M.Sugita, K.Usui, H.Shimizu, H.Suzuki, M.Terayama, K.Kanda, A.

(2011) Bioorg.Med.Chem. 19: 1930-1949

  • DOI: 10.1016/j.bmc.2011.01.065
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • To obtain small and efficient squalene synthase inhibitors, a flexible 2-aminobenzhydrol open form structure was designed and showed potent inhibitory activity comparable to 4,1-benzoxazepin compounds. Further chemical modification led to the discove ...

    To obtain small and efficient squalene synthase inhibitors, a flexible 2-aminobenzhydrol open form structure was designed and showed potent inhibitory activity comparable to 4,1-benzoxazepin compounds. Further chemical modification led to the discovery of a novel template with a strong squalene synthase inhibitory activity, and its basic structure-activity relationship was revealed. The X-ray crystallographic data of compound 12 bound to the active site of squalene synthase provided an important insight into the binding mode of this alternative template that formed 11-membered ring conformations with an intramolecular hydrogen bond.


    Organizational Affiliation

    Lead Discovery and Optimization Research Laboratories I, Daiichi Sankyo Co., Ltd, 1-2-58 Hiromachi, Shinagawa-ku, Tokyo 140-8710, Japan. ichikawa.masanori.uf@daiichisankyo.co.jp




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Squalene synthase
A
340Homo sapiensMutation(s): 0 
Gene Names: FDFT1
EC: 2.5.1.21
Find proteins for P37268 (Homo sapiens)
Go to Gene View: FDFT1
Go to UniProtKB:  P37268
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
D61
Query on D61

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Download CCD File 
A
(2R,3R)-2-(carboxymethoxy)-4-{[5-(naphthalen-2-yl)pentyl]amino}-3-{[5-(naphthalen-2-yl)pentyl]oxy}-4-oxobutanoic acid
C36 H41 N O7
MMKNOJATXTZICP-KKLWWLSJSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.207 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 85.973α = 90.00
b = 59.526β = 115.71
c = 84.139γ = 90.00
Software Package:
Software NamePurpose
CrystalCleardata scaling
CrystalCleardata reduction
MOLREPphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-12-21
    Type: Initial release
  • Version 1.1: 2017-11-08
    Type: Refinement description