4EXG | pdb_00004exg

Design and synthesis of potent hydroxyethylamine (hea) bace-1 inhibitors

• PDB DOI: https://doi.org/10.2210/pdb4EXG/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-04-30 Released: 2012-10-31 
• Deposition Author(s): Borkakoti, N., Lindberg, J., Derbyshire, D.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.227 (Depositor), 0.233 (DCC) 
• R-Value Work: 
  0.178 (Depositor), 0.178 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Literature

Design and synthesis of potent hydroxyethylamine (HEA) BACE-1 inhibitors carrying prime side 4,5,6,7-tetrahydrobenzazole and 4,5,6,7-tetrahydropyridinoazole templates.

Sund, C., Belda, O., Borkakoti, N., Lindberg, J., Derbyshire, D., Vrang, L., Hamelink, E., Hgren, C., Woestenenk, E., Wikstrom, K., Eneroth, A., Lindstrom, E., Kalayanov, G.

(2012) Bioorg Med Chem Lett 22: 6721-6727

• PubMed: 23010268 
• DOI: https://doi.org/10.1016/j.bmcl.2012.08.097
• Primary Citation Related Structures: 
  4EWO, 4EXG


• PubMed Abstract: 
  

  A set of low molecular weight compounds containing a hydroxyethylamine (HEA) core structure with different prime side alkyl substituted 4,5,6,7-tetrahydrobenzazoles and one 4,5,6,7-tetrahydropyridinoazole was synthesized. Striking differences were observed on potencies in the BACE-1 enzymatic and cellular assays depending on the nature of the heteroatoms in the bicyclic ring, from the low active compound 4 to inhibitor 6, displaying BACE-1 IC(50) values of 44 nM (enzyme assay) and 65 nM (cell-based assay).

---

Organizational Affiliation: 
• Medivir AB, Lunastigen 7, SE-14144 Huddinge, Sweden.

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: 43.48 kDa 
• Atom Count: 3,504 
• Modeled Residue Count: 377 
• Deposited Residue Count: 386 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-secretase 1	A	386	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
916	B [auth A]	N-[(2S,3R)-4-{[(4S)-6-(2,2-dimethylpropyl)-2,2-dimethyl-3,4-dihydro-2H-thieno[2,3-b]pyran-4-yl]amino}-3-hydroxy-1-phenylbutan-2-yl]acetamide C26 H38 N2 O3 S YLIBYDKWVPKMKX-RJGXRXQPSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.227 (Depositor), 0.233 (DCC) 
• R-Value Work:  0.178 (Depositor), 0.178 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.223	α = 90
b = 76.371	β = 90
c = 104.377	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
DNA	data collection
MOSFLM	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-10-31 
Deposition Author(s): Borkakoti, N., Lindberg, J., Derbyshire, D.

Revision History  

• Version 1.0: 2012-10-31
  Type: Initial release
  
• Version 1.1: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary