3WB4

Crystal Structure of beta secetase in complex with 2-amino-3,6-dimethyl-6-(2-phenylethyl)-3,4,5,6-tetrahydropyrimidin-4-one

• PDB DOI:  https://doi.org/10.2210/pdb3WB4/pdb

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


• Deposited: 2013-05-13 Released: 2013-10-02 
• Deposition Author(s): Yonezawa, S., Fujiwara, K., Yamamoto, T., Hattori, K., Yamakawa, H., Muto, C., Hosono, M., Tanaka, Y., Nakano, T., Takemoto, H., Arisawa, M., Shuto, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.254 
• R-Value Work: 0.211 
• R-Value Observed: 0.213 

Literature

Conformational restriction approach to beta-secretase (BACE1) inhibitors III: Effective investigation of the binding mode by combinational use of X-ray analysis, isothermal titration calorimetry and theoretical calculations

Yonezawa, S., Fujiwara, K., Yamamoto, T., Hattori, K., Yamakawa, H., Muto, C., Hosono, M., Tanaka, Y., Nakano, T., Takemoto, H., Arisawa, M., Shuto, S.

(2013) Bioorg Med Chem 21: 6506-6522

• PubMed: 24051074 
• DOI: https://doi.org/10.1016/j.bmc.2013.08.036
• Primary Citation of Related Structures:  
  3WB4, 3WB5


• PubMed Abstract: 
  

For further investigation of BACE1 inhibitors using conformational restriction with sp(3) hybridized carbon, we applied this approach to 6-substituted aminopyrimidone derivatives 3 to improve the inhibitory activity by reducing the entropic energy loss upon binding to BACE1. Among eight stereoisomers synthesized, [trans-(1'R,2'R),6S] isomer 6 exhibited the best BACE1 inhibitory activity, which was statistically superior to that of the corresponding ethylene linker compound (R)-3. Combinational examinations of the binding mode of 6 were performed, which included isothermal titration calorimetry (ITC), X-ray crystallographic structure analysis and theoretical calculations, to clarify the effect of our conformational restriction approach. From the ITC measurement, the binding entropy of 6 was found to be ∼0.5kcal larger than that of (R)-3, which is considered to be affected by conformational restriction with a cyclopropane ring.

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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; Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan. Electronic address: [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: 47.26 kDa 
• Atom Count: 2,854 
• Modelled Residue Count: 360 
• Deposited Residue Count: 416 
• Unique protein chains: 1

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
0B3	H [auth A]	(6R)-2-amino-3,6-dimethyl-6-(2-phenylethyl)-5,6-dihydropyrimidin-4(3H)-one C14 H19 N3 O NHJCZSSEYRWDOJ-CQSZACIVSA-N
IOD	F [auth A], G [auth A]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M
GOL	B [auth A], C [auth A], D [auth A], E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
0B3	PDBBind:  3WB4	Kd: 3.66e+4 (nM) from 1 assay(s)
	Binding MOAD:  3WB4	Kd: 3.66e+4 (nM) from 1 assay(s)
	BindingDB:  3WB4	IC50: 3.40e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.254 
• R-Value Work: 0.211 
• R-Value Observed: 0.213 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.208	α = 90
b = 102.208	β = 90
c = 169.984	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-10-02 
Deposition Author(s): Yonezawa, S., Fujiwara, K., Yamamoto, T., Hattori, K., Yamakawa, H., Muto, C., Hosono, M., Tanaka, Y., Nakano, T., Takemoto, H., Arisawa, M., Shuto, S.

Revision History  

• Version 1.0: 2013-10-02
  Type: Initial release
  
• Version 1.1: 2013-10-23
  Changes: Database references
• Version 1.2: 2017-11-22
  Changes: Refinement description