3LNK

Structure of BACE bound to SCH743813

• PDB DOI: https://doi.org/10.2210/pdb3LNK/pdb

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


• Deposited: 2010-02-02 Released: 2010-04-14 
• Deposition Author(s): Orth, P., Cumming, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.215 
• R-Value Work: 0.183 

Starting Model: experimental

Literature

Piperazine sulfonamide BACE1 inhibitors: design, synthesis, and in vivo characterization.

Cumming, J., Babu, S., Huang, Y., Carrol, C., Chen, X., Favreau, L., Greenlee, W., Guo, T., Kennedy, M., Kuvelkar, R., Le, T., Li, G., McHugh, N., Orth, P., Ozgur, L., Parker, E., Saionz, K., Stamford, A., Strickland, C., Tadesse, D., Voigt, J., Zhang, L., Zhang, Q.

(2010) Bioorg Med Chem Lett 20: 2837-2842

• PubMed: 20347593 
• DOI: https://doi.org/10.1016/j.bmcl.2010.03.050
• Primary Citation of Related Structures:  
  3LNK, 3LPI, 3LPJ, 3LPK


• PubMed Abstract: 
  

  With collaboration between chemistry, X-ray crystallography, and molecular modeling, we designed and synthesized a series of novel piperazine sulfonamide BACE1 inhibitors. Iterative exploration of the non-prime side and S2' sub-pocket of the enzyme culminated in identification of an analog that potently lowers peripheral Abeta(40) in transgenic mice with a single subcutaneous dose.

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Organizational Affiliation: 

Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, NJ 07033, USA. [e-mail]

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)

Macromolecule Content

• Total Structure Weight: 89.59 kDa 
• Atom Count: 7,066 
• Modelled Residue Count: 774 
• Deposited Residue Count: 790 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-secretase 1	A, B	395	Homo sapiens	Mutation(s): 0  Gene Names: BACE, BACE1, 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
74A	C [auth A], E [auth B]	N'-{(1S,2S)-1-(3,5-difluorobenzyl)-2-hydroxy-2-[(2R)-4-(phenylcarbonyl)piperazin-2-yl]ethyl}-5-methyl-N,N-dipropylbenzene-1,3-dicarboxamide C35 H42 F2 N4 O4 ZJLWDMHHAMNWRK-QAXCHELISA-N
TLA	D [auth A], F [auth B]	L(+)-TARTARIC ACID C4 H6 O6 FEWJPZIEWOKRBE-JCYAYHJZSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
74A	PDBBind:  3LNK	IC50: 1150 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.215 
• R-Value Work: 0.183 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.364	α = 90
b = 89.37	β = 90
c = 131.511	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
AMoRE	phasing
BUSTER	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-04-14 
Deposition Author(s): Orth, P., Cumming, J.

Revision History  

• Version 1.0: 2010-04-14
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-11-06
  Changes: Structure summary