Human Squalene synthase in complex with N-[(3R,5S)-7-Chloro-5-(2,3-dimethoxyphenyl)-1-neopentyl-2-oxo-1,2,3,5-tetrahydro-4,1-benzoxazepine-3-acetyl]-L-aspartic acid

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 

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Ligand Structure Quality Assessment 

This is version 1.2 of the entry. See complete history


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: https://doi.org/10.1016/j.bmc.2011.01.065
  • Primary Citation of Related Structures:  
    3ASX, 3Q2Z, 3Q30

  • 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 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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Squalene synthase340Homo sapiensMutation(s): 0 
Gene Names: FDFT1
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
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on D9A

Download Ideal Coordinates CCD File 
C [auth A]N-{[(3R,5S)-7-chloro-5-(2,3-dimethoxyphenyl)-1-(2,2-dimethylpropyl)-2-oxo-1,2,3,5-tetrahydro-4,1-benzoxazepin-3-yl]acetyl}-L-aspartic acid
C28 H33 Cl N2 O9
Query on PO4

Download Ideal Coordinates CCD File 
O4 P
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.604α = 90
b = 60.571β = 117.59
c = 87.028γ = 90
Software Package:
Software NamePurpose
CrystalCleardata reduction
CrystalCleardata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-12-21
    Type: Initial release
  • Version 1.1: 2017-11-08
    Changes: Refinement description
  • Version 1.2: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description