3ASX

Human Squalene synthase in complex with 1-{4-[{4-chloro-2-[(2-chlorophenyl)(hydroxy)methyl]phenyl}(2,2-dimethylpropyl)amino]-4-oxobutanoyl}piperidine-3-carboxylic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.177 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 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: 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


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
PHAROS:  P37268
GTEx:  ENSG00000079459 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP37268
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
D99
Query on D99

Download Ideal Coordinates CCD File 
C [auth A](3R)-1-{4-[{4-chloro-2-[(S)-(2-chlorophenyl)(hydroxy)methyl]phenyl}(2,2-dimethylpropyl)amino]-4-oxobutanoyl}piperidine-3-carboxylic acid
C28 H34 Cl2 N2 O5
SGSZXPGOMQXFLD-WXTAPIANSA-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
D99 PDBBind:  3ASX IC50: 20 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.177 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.069α = 90
b = 59.837β = 116.66
c = 85.447γ = 90
Software Package:
Software NamePurpose
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



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: 2017-10-11
    Changes: Refinement description
  • Version 1.2: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description