3DV1

Crystal structure of human beta-secretase in complex with NVP-ARV999

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.223 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history. 


Literature

Macrocyclic peptidomimetic beta-secretase (BACE-1) inhibitors with activity in vivo.

Machauer, R., Laumen, K., Veenstra, S., Rondeau, J.M., Tintelnot-Blomley, M., Betschart, C., Jaton, A.L., Desrayaud, S., Staufenbiel, M., Rabe, S., Paganetti, P., Neumann, U.

(2009) Bioorg Med Chem Lett 19: 1366-1370

  • DOI: https://doi.org/10.1016/j.bmcl.2009.01.055
  • Primary Citation of Related Structures:  
    3DV1, 3DV5

  • PubMed Abstract: 

    • The macrocyclic peptidic BACE-1 inhibitors 2a-c show moderate enzymatic and cellular activity. By exchange of the hydroxyethylene- to ethanolamine-transition state mimetic the peptidic character was reduced, providing the highly potent and selective inhibitor 3 ...

    The macrocyclic peptidic BACE-1 inhibitors 2a-c show moderate enzymatic and cellular activity. By exchange of the hydroxyethylene- to ethanolamine-transition state mimetic the peptidic character was reduced, providing the highly potent and selective inhibitor 3. Variation of the P' moiety resulted in the macrocyclic inhibitor 14. Both macrocycles show inhibition of BACE-1 in the brain of APP51/16 transgenic mice, 3 (NB-544) after intravenous and 14 (NB-533) after oral application.

    Related Citations: 
    • Structure-based design and synthesis of macrocyclic peptidomimetic beta-secretase (BACE-1) inhibitors.
      Machauer, R., Veenstra, S., Rondeau, J.M., Tintelnot-Blomley, M., Betschart, C., Neumann, U., Paganetti, P.
      (2009) Bioorg Med Chem Lett --: --
    Organizational Affiliation: 

    Novartis Institutes for BioMedical Research, Novartis Pharma AG, PO Box, CH-4002 Basel, Switzerland.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-secretase 1
A, B, C
402Homo 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
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AR9
Query on AR9
Download Ideal Coordinates CCD File 
D [auth A],
E [auth B],
F [auth C]		(2R,4S)-N-butyl-4-[(2S,5S,7R)-2,7-dimethyl-3,15-dioxo-1,4-diazacyclopentadecan-5-yl]-4-hydroxy-2-methylbutanamide
C24 H45 N3 O4
ZUIGWVKXPZANDI-MJCUULBUSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
AR9 PDBBind:  3DV1 IC50: 590 (nM) from 1 assay(s)
BindingDB:  3DV1 IC50: min: 590, max: 1.00e+4 (nM) from 2 assay(s)
Binding MOAD:  3DV1 IC50: 590 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.223 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.027α = 90
b = 102.945β = 103.66
c = 99.916γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACTdata extraction
MAR345data collection
CNXphasing
CNXrefinement

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-02-24
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Refinement description
  • Version 1.3: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description