6JT3 | pdb_00006jt3

Crystal Structure of BACE1 in complex with N-{3-[(4R,5R,6R)-2-amino-5-fluoro-4,6-dimethyl-5,6-dihydro-4H-1,3-thiazin-4-yl]-4-fluorophenyl}-5-(fluoromethoxy)pyrazine-2-carboxamide

• PDB DOI: https://doi.org/10.2210/pdb6JT3/pdb

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


• Deposited: 2019-04-08 Released: 2019-10-30 
• Deposition Author(s): Tadano, G., Komano, K., Yoshida, S., Suzuki, S., Nakahara, K., Fuchino, K., Fujimoto, K., Matsuoka, E., Yamamoto, T., Asada, N., Ito, H., Sakaguchi, G., Kanegawa, N., Kido, Y., Ando, S., Fukushima, T., Teisman, A., Urmaliya, V., Dhuyvetter, D., Borghys, H., Bergh, A.V.D., Austin, N., Gijsen, H.J.M., Yamano, Y., Iso, Y., Kusakabe, K.I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.242 (Depositor), 0.247 (DCC) 
• R-Value Work: 
  0.187 (Depositor), 0.193 (DCC) 
• R-Value Observed: 
  0.189 (Depositor) 

Starting Model: experimental

Literature

Discovery of an Extremely Potent Thiazine-Based beta-Secretase Inhibitor with Reduced Cardiovascular and Liver Toxicity at a Low Projected Human Dose.

Tadano, G., Komano, K., Yoshida, S., Suzuki, S., Nakahara, K., Fuchino, K., Fujimoto, K., Matsuoka, E., Yamamoto, T., Asada, N., Ito, H., Sakaguchi, G., Kanegawa, N., Kido, Y., Ando, S., Fukushima, T., Teisman, A., Urmaliya, V., Dhuyvetter, D., Borghys, H., Van Den Bergh, A., Austin, N., Gijsen, H.J.M., Yamano, Y., Iso, Y., Kusakabe, K.I.

(2019) J Med Chem 62: 9331-9337

• PubMed: 31549838 
• DOI: https://doi.org/10.1021/acs.jmedchem.9b01140
• Primary Citation Related Structures: 
  6JT3


• PubMed Abstract: 
  

  Genetic evidence points to deposition of amyloid-β (Aβ) as a causal factor for Alzheimer's disease. Aβ generation is initiated when β-secretase (BACE1) cleaves the amyloid precursor protein. Starting with an oxazine lead 1 , we describe the discovery of a thiazine-based BACE1 inhibitor 5 with robust Aβ reduction in vivo at low concentrations, leading to a low projected human dose of 14 mg/day where 5 achieved sustained Aβ reduction of 80% at trough level.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly Evidence: fluorescence resonance energy transfer

Macromolecule Content 

• Total Structure Weight: 47.24 kDa 
• Atom Count: 3,188 
• Modeled Residue Count: 379 
• 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 GTEx:  ENSG00000186318

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
C83 (Subject of Investigation/LOI)	F [auth A]	N-[3-[(4R,5R,6R)-2-azanyl-5-fluoranyl-4,6-dimethyl-5,6-dihydro-1,3-thiazin-4-yl]-4-fluoranyl-phenyl]-5-(fluoranylmethoxy)pyrazine-2-carboxamide C18 H18 F3 N5 O2 S JWJQXZNLFNMIHE-AHRODOEDSA-N
IOD	B [auth A], C [auth A]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M
GOL	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
DMS	E [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
C83	BindingDB:  6JT3	Ki: 0.34 (nM) from 1 assay(s)
		IC50: min: 0.38, max: 5 (nM) from 4 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.242 (Depositor), 0.247 (DCC) 
• R-Value Work:  0.187 (Depositor), 0.193 (DCC) 
• R-Value Observed: 0.189 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.21	α = 90
b = 101.21	β = 90
c = 171.351	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-10-30 
Deposition Author(s): Tadano, G., Komano, K., Yoshida, S., Suzuki, S., Nakahara, K., Fuchino, K., Fujimoto, K., Matsuoka, E., Yamamoto, T., Asada, N., Ito, H., Sakaguchi, G., Kanegawa, N., Kido, Y., Ando, S., Fukushima, T., Teisman, A., Urmaliya, V., Dhuyvetter, D., Borghys, H., Bergh, A.V.D., Austin, N., Gijsen, H.J.M., Yamano, Y., Iso, Y., Kusakabe, K.I.

Revision History  

• Version 1.0: 2019-10-30
  Type: Initial release
  
• Version 1.1: 2019-11-06
  Changes: Data collection, Database references
• Version 1.2: 2023-11-22
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-11-06
  Changes: Structure summary