3ZLQ

BACE2 XAPERONE COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.241 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Beta-Secretase (Bace1) Inhibitors with High in Vivo Efficacy Suitable for Clinical Evaluation in Alzheimer'S Disease.

Hilpert, H.Guba, W.Woltering, T.J.Wostl, W.Pinard, E.Mauser, H.Mayweg, A.V.Rogers-Evans, M.Humm, R.Krummenacher, D.Muser, T.Schnider, C.Jacobsen, H.Ozmen, L.Bergadano, A.Banner, D.W.Hochstrasser, R.Kuglstatter, A.David-Pierson, P.Fischer, H.Polara, A.Narquizian, R.

(2013) J Med Chem 56: 3980

  • DOI: https://doi.org/10.1021/jm400225m
  • Primary Citation of Related Structures:  
    3ZLQ, 3ZMG, 4J0P, 4J0T, 4J0V, 4J0Y, 4J0Z, 4J17, 4J1C, 4J1E, 4J1F, 4J1H, 4J1I, 4J1K

  • PubMed Abstract: 

    An extensive fluorine scan of 1,3-oxazines revealed the power of fluorine(s) to lower the pKa and thereby dramatically change the pharmacological profile of this class of BACE1 inhibitors. The CF3 substituted oxazine 89, a potent and highly brain penetrant BACE1 inhibitor, was able to reduce significantly CSF Aβ40 and 42 in rats at oral doses as low as 1 mg/kg. The effect was long lasting, showing a significant reduction of Aβ40 and 42 even after 24 h. In contrast to 89, compound 1b lacking the CF3 group was virtually inactive in vivo.


  • Organizational Affiliation

    Discovery Chemistry, Pharma Research & Early Development, Grenzacherstrasse 124, Basel CH-4070, Switzerland. hans.hilpert@roche.com


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
BETA-SECRETASE 2
A, B
386Homo sapiensMutation(s): 1 
EC: 3.4.23.45
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y5Z0 (Homo sapiens)
Explore Q9Y5Z0 
Go to UniProtKB:  Q9Y5Z0
PHAROS:  Q9Y5Z0
GTEx:  ENSG00000182240 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y5Z0
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
XA4813
C, D
122Lama glamaMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
6T9
Query on 6T9

Download Ideal Coordinates CCD File 
E [auth A],
F [auth B]
5-Ethoxy-pyridine-2-carboxylic acid [3-((R)-2-amino-5,5-difluoro-4-methyl-5,6-dihydro-4H-[1,3]oxazin-4-yl)-4-fluoro-phenyl]-amide
C19 H19 F3 N4 O3
DWKGLYKXNUIYDM-GOSISDBHSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
6T9 PDBBind:  3ZLQ IC50: 904 (nM) from 1 assay(s)
BindingDB:  3ZLQ IC50: 904 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.241 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.78α = 90
b = 210.983β = 105.07
c = 53.303γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
REFMACphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-05-01
    Type: Initial release
  • Version 1.1: 2013-05-22
    Changes: Atomic model, Derived calculations, Other
  • Version 1.2: 2013-06-05
    Changes: Database references