Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 47.64 kDa 
• Atom Count: 3030 
• Modelled Residue Count: 360 
• Deposited Residue Count: 416 
• Unique protein chains: 1

3VV6

Crystal Structure of beta secetase in complex with 2-amino-3-methyl-6-((1S, 2R)-2-phenylcyclopropyl)pyrimidin-4(3H)-one

• PDB DOI: 10.2210/pdb3VV6/pdb

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


• Deposited: 2012-07-17 Released: 2012-10-24 
• Deposition Author(s): Yonezawa, S., Yamamoto, T., Yamakawa, H., Muto, C., Hosono, M., Hattori, K., Higashino, K., Sakagami, M., Togame, H., Tanaka, Y., Nakano, T., Takemoto, H., Arisawa, M., Shuto, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.280 
• R-Value Work: 0.249 
• R-Value Observed: 0.250 

Literature

Conformational restriction approach to beta-secretase (BACE1) inhibitors: effect of a cyclopropane ring to induce an alternative binding mode

Yonezawa, S., Yamamoto, T., Yamakawa, H., Muto, C., Hosono, M., Hattori, K., Higashino, K., Yutsudo, T., Iwamoto, H., Kondo, Y., Sakagami, M., Togame, H., Tanaka, Y., Nakano, T., Takemoto, H., Arisawa, M., Shuto, S.

(2012) J Med Chem 55: 8838-8858

• PubMed: 22998419 
• DOI: 10.1021/jm3011405
• Primary Citation of Related Structures:  
  3VV6, 3VV7, 3VV8


• PubMed Abstract: 
  

Improvement of a drug's binding activity using the conformational restriction approach with sp³ hybridized carbon is becoming a key strategy in drug discovery. We applied this approach to BACE1 inhibitors and designed four stereoisomeric cyclopropane compounds in which the ethylene linker of a known amidine-type inhibitor 2 was replaced with chiral cyclopropane rings. The synthesis and biologic evaluation of these compounds revealed that the cis-(1S,2R) isomer 6 exhibited the most potent BACE1 inhibitory activity among them. X-ray structure analysis of the complex of 6 and BACE1 revealed that its unique binding mode is due to the apparent CH-π interaction between the rigid cyclopropane ring and the Tyr71 side chain. A derivatization study using 6 as a lead molecule led to the development of highly potent inhibitors in which the structure-activity relationship as well as the binding mode of the compounds clearly differ from those of known amidine-type inhibitors.

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Organizational Affiliation: 

Shionogi Innovation Center for Drug Discovery, Shionogi & Co., Ltd., Kita-21 Nishi-11 Kita-ku, Sapporo 001-0021, Japan. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-secretase 1	A	416	Homo sapiens	Mutation(s): 0  Gene Names: BACE1, BACE, KIAA1149 EC: 3.4.23.46
UniProt & NIH Common Fund Data Resources
Find proteins for P56817 (Homo sapiens) Explore P56817  Go to UniProtKB:  P56817
PHAROS:  P56817

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
B00	K [auth A]	2-amino-3-methyl-6-[(1S,2R)-2-phenylcyclopropyl]pyrimidin-4(3H)-one C14 H15 N3 O VTVXXFGROBMFAL-QWRGUYRKSA-N
IOD	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M
GOL	G [auth A], H [auth A], I [auth A], J [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
B00	BindingDB:  3VV6	IC50: 1.57e+5 (nM) from 1 assay(s)
	PDBBind:  3VV6	IC50: 1.57e+5 (nM) from 1 assay(s)
	Binding MOAD:  3VV6	IC50: 1.57e+5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.280 
• R-Value Work: 0.249 
• R-Value Observed: 0.250 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.491	α = 90
b = 102.491	β = 90
c = 170.156	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-07-17 
• Released Date: 2012-10-24 
Deposition Author(s): Yonezawa, S., Yamamoto, T., Yamakawa, H., Muto, C., Hosono, M., Hattori, K., Higashino, K., Sakagami, M., Togame, H., Tanaka, Y., Nakano, T., Takemoto, H., Arisawa, M., Shuto, S.

Revision History  

• Version 1.0: 2012-10-24
  Type: Initial release
  
• Version 1.1: 2013-09-04
  Changes: Database references
• Version 1.2: 2017-11-22
  Changes: Refinement description