Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Protein Workshop | Ligand Explorer

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

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

Macromolecule Content

• Total Structure Weight: 47637.23 
• Atom Count: 2820 
• 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

• DOI: 10.2210/pdb3VV6/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli


• 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 

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:  
  3VV8, 3VV7


• 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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Beta-secretase 1	A	416	Homo sapiens	Mutation(s): 0  Gene Names: BACE1 (BACE, KIAA1149) EC: 3.4.23.46
Find proteins for P56817 (Homo sapiens) Go to Gene View: BACE1 Go to UniProtKB:  P56817

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
IOD	A	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M
GOL	A	GLYCEROL GLYCERIN; PROPANE-1,2,3-TRIOL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
B00	A	2-amino-3-methyl-6-[(1S,2R)-2-phenylcyclopropyl]pyrimidin-4(3H)-one C14 H15 N3 O VTVXXFGROBMFAL-QWRGUYRKSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
B00	IC50: 157000 nM (100) BINDINGDB
B00	IC50: 157000 nM BINDINGMOAD
B00	IC50: 157000 nM PDBBIND

Experimental Data & Validation

Experimental Data

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

Unit Cell:

Length (Å)	Angle (°)
a = 102.491	α = 90.00
b = 102.491	β = 90.00
c = 170.156	γ = 120.00

Software Package:

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

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
  Type: Database references
• Version 1.2: 2017-11-22
  Type: Refinement description