2ZJL

Crystal structure of the human BACE1 catalytic domain in complex with N-[1-(5-bromo-2,3-dimethoxy-benzyl)-piperidin-4-yl]-4-mercapto-butyramide

• PDB DOI: https://doi.org/10.2210/pdb2ZJL/pdb

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


• Deposited: 2008-03-07 Released: 2009-01-20 
• Deposition Author(s): Randal, M., Lam, M.B., Lu, W., Romanowski, M.J.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.291 
• R-Value Work: 0.258 
• R-Value Observed: 0.260 

Starting Model: experimental

Literature

Fragment-based discovery of novel BACE1 inhibitors using Tethering technology

Yang, W., Fucini, R.V., Fahr, B.T., Randal, M., Lind, K.E., Lam, M.B., Lu, W., Lu, Y., Cary, D.R., Romanowski, M.J.

To be published.

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: 45.67 kDa 
• Atom Count: 2,964 
• Modelled Residue Count: 344 
• Deposited Residue Count: 405 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-secretase 1	A	405	Homo sapiens	Mutation(s): 1  Gene Names: BACE1 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
F1L	B [auth A]	N-[1-(5-bromo-2,3-dimethoxybenzyl)piperidin-4-yl]-4-sulfanylbutanamide C18 H27 Br N2 O3 S HESMISSJMKCCAV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.291 
• R-Value Work: 0.258 
• R-Value Observed: 0.260 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.091	α = 90
b = 104.091	β = 90
c = 167.98	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
CrystalClear	data collection
d*TREK	data reduction
d*TREK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-01-20 
Deposition Author(s): Randal, M., Lam, M.B., Lu, W., Romanowski, M.J.

Revision History  

• Version 1.0: 2009-01-20
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2021-11-10
  Changes: Database references, Derived calculations
• Version 1.3: 2023-11-01
  Changes: Data collection, Refinement description
• Version 1.4: 2024-11-20
  Changes: Structure summary