5TOL | pdb_00005tol

CRYSTAL STRUCTURE OF BETA-SITE APP-CLEAVING ENZYME 1 COMPLEXED WITH N-(3-((4AS,7AS)-2-AMINO-4,4A,5,6-TETRAHYDRO-7AH-FURO[2,3-D][1,3]THIAZIN-7A-YL)-4-FLUOROPHENYL)-5-BROMO-2-PYRIDINECARBOXAMIDE

• PDB DOI: https://doi.org/10.2210/pdb5TOL/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2016-10-18 Released: 2016-11-23 
• Deposition Author(s): Muckelbauer, J.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.51 Å
• R-Value Free: 
  0.257 (Depositor), 0.249 (DCC) 
• R-Value Work: 
  0.201 (Depositor), 0.199 (DCC) 
• R-Value Observed: 
  0.204 (Depositor) 

Literature

Discovery of furo[2,3-d][1,3]thiazinamines as beta amyloid cleaving enzyme-1 (BACE1) inhibitors.

Wu, Y.J., Guernon, J., Rajamani, R., Toyn, J.H., Ahlijanian, M.K., Albright, C.F., Muckelbauer, J., Chang, C., Camac, D., Macor, J.E., Thompson, L.A.

(2016) Bioorg Med Chem Lett 26: 5729-5731

• PubMed: 27816517 
• DOI: https://doi.org/10.1016/j.bmcl.2016.10.055
• Primary Citation Related Structures: 
  5TOL


• PubMed Abstract: 
  

  This Letter describes the synthesis and structure-activity relationships of a series of furo[2,3-d][1,3]thiazinamine BACE1 inhibitors. The co-crystal structure of a representative thiazinamine 2e bound with the BACE1 active site displayed a binding mode driven by interactions with the catalytic aspartate dyad and engagement of the biaryl amide toward the S1 and S3 pockets. This work indicates that furo[2,3-d]thiazine can serve as a viable bioisostere of the known furo[3,4-d]thiazine.

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Organizational Affiliation: 
• Research and Development, Bristol-Myers Squibb, 5 Research Parkway, Wallingford, CT 06492, USA. Electronic address: [e-mail].
Research and Development, Bristol-Myers Squibb, 5 Research Parkway, Wallingford, CT 06492, USA.
Research and Development, Bristol-Myers Squibb, PO Box 4000, Princeton, NJ 08543, USA.

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: 46.37 kDa 
• Atom Count: 2,997 
• Modeled Residue Count: 374 
• Deposited Residue Count: 412 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-secretase 1	A	412	Homo sapiens	Mutation(s): 2  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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
7H3	B [auth A]	N-{3-[(4aR,7aR)-2-amino-4,4a,5,6-tetrahydro-7aH-furo[2,3-d][1,3]thiazin-7a-yl]-4-fluorophenyl}-5-bromopyridine-2-carboxamide C18 H16 Br F N4 O2 S DACRJCISVSMZQT-XTZNXHDOSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
7H3	BindingDB:  5TOL	IC50: 33 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.51 Å
• R-Value Free:  0.257 (Depositor), 0.249 (DCC) 
• R-Value Work:  0.201 (Depositor), 0.199 (DCC) 
• R-Value Observed: 0.204 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.49	α = 90
b = 101.49	β = 90
c = 171.237	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-11-23 
Deposition Author(s): Muckelbauer, J.K.

Revision History  

• Version 1.0: 2016-11-23
  Type: Initial release
  
• Version 1.1: 2016-12-07
  Changes: Database references
• Version 1.2: 2024-11-06
  Changes: Data collection, Database references, Structure summary