3BUH | pdb_00003buh

BACE-1 complexed with compound 4

• PDB DOI: https://doi.org/10.2210/pdb3BUH/pdb

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


• Deposited: 2008-01-02 Released: 2008-03-11 
• Deposition Author(s): Kuglstatter, A., Hennig, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.238 (Depositor) 
• R-Value Work: 
  0.199 (Depositor) 
• R-Value Observed: 
  0.201 (Depositor) 

Literature

Tyramine fragment binding to BACE-1

Kuglstatter, A., Stahl, M., Peters, J.U., Huber, W., Stihle, M., Schlatter, D., Benz, J., Ruf, A., Roth, D., Enderle, T., Hennig, M.

(2008) Bioorg Med Chem Lett 18: 1304-1307

• PubMed: 18226904 
• DOI: https://doi.org/10.1016/j.bmcl.2008.01.032
• Primary Citation Related Structures: 
  3BRA, 3BUF, 3BUG, 3BUH


• PubMed Abstract: 
  

  Fragment screening revealed that tyramine binds to the active site of the Alzheimer's disease drug target BACE-1. Hit expansion by selection of compounds from the Roche compound library identified tyramine derivatives with improved binding affinities as monitored by surface plasmon resonance. X-ray structures show that the amine of the tyramine fragment hydrogen-bonds to the catalytic water molecule. Structure-guided ligand design led to the synthesis of further low molecular weight compounds that are starting points for chemical leads.

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Organizational Affiliation: 
• F. Hoffmann-La Roche, Pharma Research Basel, Grenzacherstr., 4070 Basel, Switzerland.

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: 45.77 kDa 
• Atom Count: 3,103 
• Modeled Residue Count: 370 
• Deposited Residue Count: 409 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
beta-secretase 1	A	409	Homo sapiens	Mutation(s): 1  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
AED	B [auth A]	4-(2-aminoethyl)-2-cyclohexylphenol C14 H21 N O DOCCSEDGBYCYLS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
AED	BindingDB:  3BUH	Kd: 2.20e+5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.238 (Depositor) 
• R-Value Work:  0.199 (Depositor) 
• R-Value Observed: 0.201 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.491	α = 90
b = 102.491	β = 90
c = 170.063	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-03-11 
Deposition Author(s): Kuglstatter, A., Hennig, M.

Revision History  

• Version 1.0: 2008-03-11
  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: 2024-10-30
  Changes: Data collection, Structure summary