3N4L

BACE-1 in complex with ELN380842

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.226 

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Literature

Improving the permeability of the hydroxyethylamine BACE-1 inhibitors: structure-activity relationship of P2' substituents.

Truong, A.P., Probst, G.D., Aquino, J., Fang, L., Brogley, L., Sealy, J.M., Hom, R.K., Tucker, J.A., John, V., Tung, J.S., Pleiss, M.A., Konradi, A.W., Sham, H.L., Dappen, M.S., Toth, G., Yao, N., Brecht, E., Pan, H., Artis, D.R., Ruslim, L., Bova, M.P., Sinha, S., Yednock, T.A., Zmolek, W., Quinn, K.P., Sauer, J.M.

(2010) Bioorg Med Chem Lett 20: 4789-4794

  • DOI: https://doi.org/10.1016/j.bmcl.2010.06.112
  • Primary Citation of Related Structures:  
    3N4L

  • PubMed Abstract: 

    • Herein we describe further evolution of hydroxyethylamine inhibitors of BACE-1 with enhanced permeability characteristics necessary for CNS penetration. Variation at the P2' position of the inhibitor with more polar substituents led to compounds 19 and 32, which retained the potency of more lipophilic analog 1 but with much higher observed passive permeability in MDCK cellular assay ...

    Herein we describe further evolution of hydroxyethylamine inhibitors of BACE-1 with enhanced permeability characteristics necessary for CNS penetration. Variation at the P2' position of the inhibitor with more polar substituents led to compounds 19 and 32, which retained the potency of more lipophilic analog 1 but with much higher observed passive permeability in MDCK cellular assay.

    Organizational Affiliation: 

    Department of Medicinal Chemistry, Elan Pharmaceuticals, 180 Oyster Point Boulevard, South San Francisco, CA 94080, United States.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-secretase 1
A, B, C
406Homo sapiensMutation(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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP56817
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
842
Query on 842
Download Ideal Coordinates CCD File 
D [auth A],
E [auth B],
F [auth C]		N-[(1S,2R)-1-(3,5-difluorobenzyl)-2-hydroxy-3-({1-[3-(1H-pyrazol-1-yl)phenyl]cyclohexyl}amino)propyl]acetamide
C27 H32 F2 N4 O2
QXNFPOMRKODYSK-IZZNHLLZSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
842 PDBBind:  3N4L IC50: 59 (nM) from 1 assay(s)
BindingDB:  3N4L IC50: 59 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.226 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.047α = 90
b = 105.582β = 104.63
c = 101.575γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
MOLREPphasing
REFMACrefinement
d*TREKdata reduction
d*TREKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

  • Released Date: 2010-11-24 
    • Deposition Author(s): Yao, N.H.

Revision History  (Full details and data files)

  • Version 1.0: 2010-11-24
    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