3QI1 | pdb_00003qi1

Design and synthesis of hydroxyethylamine (hea) BACE-1 inhibitors: prime side chromane-containing inhibitors

• PDB DOI: https://doi.org/10.2210/pdb3QI1/pdb

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


• Deposited: 2011-01-26 Released: 2012-03-28 
• Deposition Author(s): Yao, N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.269 (Depositor), 0.263 (DCC) 
• R-Value Work: 
  0.198 (Depositor), 0.193 (DCC) 
• R-Value Observed: 
  0.202 (Depositor) 

Literature

Design and synthesis of hydroxyethylamine (HEA) BACE-1 inhibitors: prime side chromane-containing inhibitors.

Ng, R.A., Sun, M., Bowers, S., Hom, R.K., Probst, G.D., John, V., Fang, L.Y., Maillard, M., Gailunas, A., Brogley, L., Neitz, R.J., Tung, J.S., Pleiss, M.A., Konradi, A.W., Sham, H.L., Dappen, M.S., Adler, M., Yao, N., Zmolek, W., Nakamura, D., Quinn, K.P., Sauer, J.M., Bova, M.P., Ruslim, L., Artis, D.R., Yednock, T.A.

(2013) Bioorg Med Chem Lett 23: 4674-4679

• PubMed: 23856050 
• DOI: https://doi.org/10.1016/j.bmcl.2013.06.006
• Primary Citation Related Structures: 
  3QI1


• PubMed Abstract: 
  

  The structure activity relationship of the prime region of conformationally restricted hydroxyethylamine (HEA) BACE inhibitors is described. Variation of the P1' region provided selectivity over Cat-D with a series of 2,2-dioxo-isothiochromanes and optimization of the P2' substituent of chromane-HEA(s) with polar substituents provided improvements in the compound's in vitro permeability. Significant potency gains were observed with small aliphatic substituents such as methyl, n-propyl, and cyclopropyl when placed at the C-2 position of the chromane.

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Organizational Affiliation: 
• Department of Chemical Sciences, Elan Pharmaceuticals, 180 Oyster Point Boulevard, South San Francisco, CA 94080, USA.

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: 45.9 kDa 
• Atom Count: 3,236 
• Modeled Residue Count: 382 
• Deposited Residue Count: 408 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-secretase 1	A	408	Homo sapiens	Mutation(s): 2  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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
C6A	B [auth A]	N-[(2S,3R)-4-{[(2R,4S)-2-cyclopropyl-6-(2,2-dimethylpropyl)-3,4-dihydro-2H-chromen-4-yl]amino}-1-(3,5-difluorophenyl)-3-hydroxybutan-2-yl]acetamide C29 H38 F2 N2 O3 IBLLHMQPQAMFLM-WDTRASESSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.269 (Depositor), 0.263 (DCC) 
• R-Value Work:  0.198 (Depositor), 0.193 (DCC) 
• R-Value Observed: 0.202 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.174	α = 90
b = 75.506	β = 90
c = 80.236	γ = 90

Software Package:

Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
CrystalClear	data reduction
CrystalClear	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-03-28 
Deposition Author(s): Yao, N.

Revision History  

• Version 1.0: 2012-03-28
  Type: Initial release
  
• Version 1.1: 2013-12-18
  Changes: Database references
• Version 1.2: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary