3V66

HUMAN SQUALENE SYNTHASE IN COMPLEX WITH 2-(1-{2-[(4R,6S)-8-chloro-6-(2,3-dimethoxyphenyl)-4H,6H-pyrrolo[1,2-a][4,1]benzoxazepin-4-yl]acetyl}-4-piperidinyl)acetic acid

• PDB DOI: https://doi.org/10.2210/pdb3V66/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  OPM


• Deposited: 2011-12-18 Released: 2012-12-19 
• Deposition Author(s): Suzuki, M., Ohtsuka, M., Ohki, H., Haginoya, N., Itoh, M., Sugita, K., Usui, H., Ichikawa, M., Higashihashi, N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.224 
• R-Value Work: 0.197 
• R-Value Observed: 0.199 

Literature

Discovery of novel tricyclic compounds as squalene synthase inhibitors

Ichikawa, M., Ohtsuka, M., Ohki, H., Haginoya, N., Itoh, M., Sugita, K., Usui, H., Suzuki, M., Terayama, K., Kanda, A.

(2012) Bioorg Med Chem 20: 3072-3093

• PubMed: 22464687 
• DOI: https://doi.org/10.1016/j.bmc.2012.02.054
• Primary Citation of Related Structures:  
  3V66


• PubMed Abstract: 
  

  In the present article, we have reported the design, synthesis, and identification of highly potent benzhydrol derivatives as squalene synthase inhibitors (compound 1). Unfortunately, the in vivo efficacies of the compounds were not enough for acquiring the clinical candidate. We continued our investigation to obtain a more in vivo efficacious template than the benzhydrol template. In our effort, we focused on a benzoxazepine ring and designed a new tricyclic scaffold by the incorporation of heterocycle into it. Prepared pyrrolobenzoxazepine derivatives showed further efficient in vitro and in vivo activities.

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Organizational Affiliation: 

Lead Discovery and Optimization Research Laboratories I, R&D Division, Daiichi Sankyo Co. Ltd, 1-2-58 Hiromachi, Shinagawa-ku, Tokyo 140-8710, Japan. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 39.8 kDa 
• Atom Count: 3,048 
• Modelled Residue Count: 335 
• Deposited Residue Count: 340 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Squalene synthase	A	340	Homo sapiens	Mutation(s): 0  Gene Names: FDFT1 EC: 2.5.1.21 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P37268 (Homo sapiens) Explore P37268  Go to UniProtKB:  P37268
PHAROS:  P37268 GTEx:  ENSG00000079459

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
D3A	C [auth A]	(1-{[(4R,6S)-8-chloro-6-(2,3-dimethoxyphenyl)-4H,6H-pyrrolo[1,2-a][4,1]benzoxazepin-4-yl]acetyl}piperidin-4-yl)acetic acid C29 H31 Cl N2 O6 MSSQOQPKGAMUSY-LEAFIULHSA-N
PO4	B [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Binding Affinity Annotations
ID	Source	Binding Affinity
D3A	BindingDB:  3V66	IC50: min: 1.3, max: 2.7 (nM) from 2 assay(s)
	PDBBind:  3V66	IC50: 1.3 (nM) from 1 assay(s)
	Binding MOAD:  3V66	IC50: 1.3 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.224 
• R-Value Work: 0.197 
• R-Value Observed: 0.199 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.438	α = 90
b = 60.144	β = 117.14
c = 85.797	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CrystalClear	data reduction
CrystalClear	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-12-19 
Deposition Author(s): Suzuki, M., Ohtsuka, M., Ohki, H., Haginoya, N., Itoh, M., Sugita, K., Usui, H., Ichikawa, M., Higashihashi, N.

Revision History  

• Version 1.0: 2012-12-19
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary