6DHC | pdb_00006dhc

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

PDB DOI: https://doi.org/10.2210/pdb6DHC/pdb

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 (Depositor), 0.221 (DCC)
R-Value Work:
0.172 (Depositor), 0.175 (DCC)
R-Value Observed:
0.174 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

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

PubMed: 29970308 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1016/j.bmcl.2018.06.045
Primary Citation 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. 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 Medicinal Chemistry, Purdue University, West Lafayette, IN 47907, United States. Electronic address: akghosh@purdue.edu.

Macromolecule Content

Total Structure Weight: 149.53 kDa
Atom Count: 9,364
Modeled Residue Count: 1,135
Deposited Residue Count: 1,323
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-secretase 1	A, B, C	441	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 GTEx: ENSG00000186318
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P56817
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GHJ (Subject of Investigation/LOI) Query on GHJ Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain P [auth C] SDF format, chain K [auth B] MOL2 format, chain D [auth A] MOL2 format, chain P [auth C] MOL2 format, chain K [auth B] mmCIF format, chain D [auth A] mmCIF format, chain P [auth C] mmCIF format, chain K [auth B]	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		Interactions Focus chain D [auth A] Focus chain K [auth B] Focus chain P [auth C] Interactions & Density Focus chain D [auth A] Focus chain K [auth B] Focus chain P [auth C]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain T [auth C] MOL2 format, chain T [auth C] mmCIF format, chain T [auth C]	T [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain T [auth C] Interactions & Density Focus chain T [auth C]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain R [auth C] SDF format, chain S [auth C] SDF format, chain Q [auth C] SDF format, chain N [auth B] SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain R [auth C] mmCIF format, chain S [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	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		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C]
URE Query on URE Download:Ideal Coordinates CCD File SDF format, chain O [auth B] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] MOL2 format, chain O [auth B] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] mmCIF format, chain O [auth B] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A]	H [auth A], I [auth A], J [auth A], O [auth B]	UREA C H₄ N₂ O XSQUKJJJFZCRTK-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain O [auth B] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain O [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.85 Å
R-Value Free: 0.218 (Depositor), 0.221 (DCC)
R-Value Work: 0.172 (Depositor), 0.175 (DCC)
R-Value Observed: 0.174 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.987	α = 90
b = 103.322	β = 102.98
c = 100.959	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2018-07-25

Deposition Author(s):

Mesecar, A.D.

Lendy, E.K.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM053386

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
Version 1.3: 2024-10-23
Changes: Data collection, Database references, Structure summary