3WB4

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


Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

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

  • DOI: 10.1016/j.bmc.2013.08.036
  • Primary Citation of Related Structures:  

  • 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 lo ...

    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.


    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: shuji.yonezawa@shionogi.co.jp.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-secretase 1
A
416Homo sapiensMutation(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
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0B3
Query on 0B3

Download SDF File 
Download CCD File 
A
(6R)-2-amino-3,6-dimethyl-6-(2-phenylethyl)-5,6-dihydropyrimidin-4(3H)-one
C14 H19 N3 O
NHJCZSSEYRWDOJ-CQSZACIVSA-N
 Ligand Interaction
IOD
Query on IOD

Download SDF File 
Download CCD File 
A
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
0B3IC50: 34000 nM (100) BINDINGDB
0B3IC50: 220000 nM BINDINGMOAD
0B3Kd: 36600 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.211 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 102.208α = 90.00
b = 102.208β = 90.00
c = 169.984γ = 120.00
Software Package:
Software NamePurpose
MOLREPphasing
DENZOdata reduction
HKL-2000data scaling
PHENIXrefinement
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
CrystalCleardata collection
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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