6DHC

X-ray structure of BACE1 in complex with a bicyclic isoxazoline carboxamide as the P3 ligand

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

  • Deposited: 2018-05-19 Released: 2018-07-25 
  • Deposition Author(s): Mesecar, A.D., Lendy, E.K.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.174 

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Literature

Design, synthesis, X-ray studies, and biological evaluation of novel BACE1 inhibitors with bicyclic isoxazoline carboxamides as the P3 ligand.

Ghosh, A.K., Ghosh, K., Brindisi, M., Lendy, E.K., Yen, Y.C., Kumaragurubaran, N., Huang, X., Tang, J., Mesecar, A.D.

(2018) Bioorg Med Chem Lett 28: 2605-2610

  • DOI: https://doi.org/10.1016/j.bmcl.2018.06.045
  • Primary Citation of Related Structures:  
    6DHC

  • PubMed Abstract: 

    • We describe the design, synthesis, X-ray studies, and biological evaluation of novel BACE1 inhibitors containing bicyclic isoxazoline carboxamides as the P3 ligand in combination with methyl cysteine, methylsulfonylalanine and Boc-amino alanine as P2 ligands ...

    We describe the design, synthesis, X-ray studies, and biological evaluation of novel BACE1 inhibitors containing bicyclic isoxazoline carboxamides as the P3 ligand in combination with methyl cysteine, methylsulfonylalanine and Boc-amino alanine as P2 ligands. Inhibitor 3a displayed a BACE1 K i value of 10.9 nM and EC 50 of 343 nM. The X-ray structure of 3a bound to the active site of BACE1 was determined at 2.85 Å resolution. The structure revealed that the major molecular interactions between BACE1 and the bicyclic tetrahydrofuranyl isoxazoline heterocycle are van der Waals in nature.

    Organizational Affiliation: 

    Department of Chemistry, Purdue University, West Lafayette, IN 47907, United States; Department of Biochemistry, Purdue University, West Lafayette, IN 47907, United States; Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, United States.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-secretase 1
A, B, C
441Homo sapiensMutation(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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP56817
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GHJ (Subject of Investigation/LOI)
Query on GHJ
Download Ideal Coordinates CCD File 
D [auth A],
K [auth B],
P [auth C]		(3R,3aR,6aS)-N-[(4R,7S,8S,10R,13S)-8-hydroxy-10,17-dimethyl-7-(2-methylpropyl)-5,11,14-trioxo-13-(propan-2-yl)-2-thia-6,12,15-triazaoctadecan-4-yl]hexahydrofuro[3,2-d][1,2]oxazole-3-carboxamide
C29 H53 N5 O7 S
FHZUZMVZKPPWHG-VRUQXOILSA-N		 Ligand Interaction
SO4
Query on SO4
Download Ideal Coordinates CCD File 
T [auth C]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
GOL
Query on GOL
Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
L [auth B]
M [auth B]
E [auth A],
F [auth A],
G [auth A],
L [auth B],
M [auth B],
N [auth B],
Q [auth C],
R [auth C],
S [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
URE
Query on URE
Download Ideal Coordinates CCD File 
H [auth A],
I [auth A],
J [auth A],
O [auth B]		UREA
C H4 N2 O
XSQUKJJJFZCRTK-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.174 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.987α = 90
b = 103.322β = 102.98
c = 100.959γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM053386

Revision History  (Full details and data files)

  • Version 1.0: 2018-07-25
    Type: Initial release
  • Version 1.1: 2018-08-22
    Changes: Data collection, Database references
  • Version 1.2: 2020-01-01
    Changes: Author supporting evidence