6E3Z | pdb_00006e3z

Structure of Bace-1 in complex with Ligand 8

• PDB DOI: https://doi.org/10.2210/pdb6E3Z/pdb

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


• Deposited: 2018-07-16 Released: 2019-09-11 
• Deposition Author(s): Shaffer, P.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free: 
  0.212 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.179 (Depositor), 0.181 (DCC) 
• R-Value Observed: 
  0.179 (Depositor) 

Literature

Discovery and Chemical Development of JNJ-50138803, a Clinical Candidate BACE1 Inhibitor

Gijsen, H.J.M., Lin, J., Houpis, Y.

(2020) ACS Symp Ser Am Chem Soc 1307

• DOI: https://doi.org/10.1021/bk-2018-1307.ch004

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 146.19 kDa 
• Atom Count: 9,893 
• Modeled Residue Count: 1,130 
• Deposited Residue Count: 1,296 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-secretase 1	A, B, C	432	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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HRV	D [auth A], E [auth B], F [auth C], G [auth C]	N-{3-[(2R,3R)-5-amino-3-methyl-2-(trifluoromethyl)-3,6-dihydro-2H-1,4-oxazin-3-yl]-4-fluorophenyl}-3,5-dichloropyridine-2-carboxamide C18 H14 Cl2 F4 N4 O2 VLILPGWCHAEKPY-IAGOWNOFSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free:  0.212 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.179 (Depositor), 0.181 (DCC) 
• R-Value Observed: 0.179 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 232.178	α = 90
b = 100.5	β = 103.22
c = 63.968	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-09-11 
Deposition Author(s): Shaffer, P.L.

Revision History  

• Version 1.0: 2019-09-11
  Type: Initial release
  
• Version 1.1: 2020-03-25
  Changes: Database references
• Version 1.2: 2024-10-23
  Changes: Advisory, Data collection, Database references, Structure summary