3Q30 | pdb_00003q30

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

• PDB DOI: https://doi.org/10.2210/pdb3Q30/pdb

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


• Deposited: 2010-12-21 Released: 2011-12-21 
• Deposition Author(s): Suzuki, M., Shimizu, H., Katakura, S., Yamazaki, K., Higashihashi, N., Ichikawa, M., Yokomizo, A., Itoh, M., Sugita, K., Usui, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.237 (Depositor), 0.187 (DCC) 
• R-Value Work: 
  0.207 (Depositor), 0.196 (DCC) 
• R-Value Observed: 
  0.208 (Depositor) 

Starting Model: experimental

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

• PubMed: 21353782 
• DOI: https://doi.org/10.1016/j.bmc.2011.01.065
• Primary Citation 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.

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Organizational Affiliation: 
• Lead Discovery and Optimization Research Laboratories I, 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: 39.91 kDa 
• Atom Count: 2,949 
• Modeled Residue Count: 330 
• 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
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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
D61	D [auth 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
PO4	E [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
MG	B [auth A], C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.237 (Depositor), 0.187 (DCC) 
• R-Value Work:  0.207 (Depositor), 0.196 (DCC) 
• R-Value Observed: 0.208 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.973	α = 90
b = 59.526	β = 115.71
c = 84.139	γ = 90

Software Package:

Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
CrystalClear	data reduction
CrystalClear	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-12-21 
Deposition Author(s): Suzuki, M., Shimizu, H., Katakura, S., Yamazaki, K., Higashihashi, N., Ichikawa, M., Yokomizo, A., Itoh, M., Sugita, K., Usui, H.

Revision History  

• 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