3IXJ

Crystal structure of beta-secretase 1 in complex with selective beta-secretase 1 inhibitor

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.212 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 

Literature

Design and Synthesis of Potent and Selective BACE-1 Inhibitors.

Bjorklund, C., Oscarson, S., Benkestock, K., Borkakoti, N., Jansson, K., Lindberg, J., Vrang, L., Hallberg, A., Rosenquist, A., Samuelsson, B.

(2010) J.Med.Chem. 53: 1458-1464

  • DOI: 10.1021/jm901168f

  • PubMed Abstract: 

    • Highly potent BACE-1 protease inhibitors have been developed from an inhibitors containing a hydroxyethylene (HE) core displaying aryloxymethyl or benzyloxymethyl P1 side chain and a methoxy P1' side chain. The target molecules were synthesized in go ...

    Highly potent BACE-1 protease inhibitors have been developed from an inhibitors containing a hydroxyethylene (HE) core displaying aryloxymethyl or benzyloxymethyl P1 side chain and a methoxy P1' side chain. The target molecules were synthesized in good overall yields from chiral carbohydrate starting materials. The inhibitors show high BACE-1 potency and good selectivity against cathepsin D, where the most potent inhibitor furnishes BACE-1 K(i) < 1 nM and displays >1000-fold selectivity over cathepsin D.

    Organizational Affiliation: 

    Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-secretase 1
A, B, C
388Homo sapiensMutation(s): 0 
Gene Names: BACE1 (BACE, KIAA1149)
EC: 3.4.23.46
Find proteins for P56817 (Homo sapiens)
Go to Gene View: BACE1
Go to UniProtKB:  P56817
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
586
Query on 586
Download SDF File 
Download CCD File 
A, B, C
N-[4-(1-BENZYLCARBAMOYL-2-METHYL-PROPYLCARBAMOYL)-1-(3,5-DIFLUORO-PHENOXYMETHYL)-2-HYDROXY-4-METHOXY-BUTYL]-5-(METHANESULFONYL-METHYL-AMINO)-N'-(1-PHENYLETHYL)-ISOPHTHALAMIDE
N-{(1S,2S,4R)-5-{[(1S)-1-(benzylcarbamoyl)-2-methylpropyl]amino}-1-[(3,5-difluorophenoxy)methyl]-2-hydroxy-4-methoxy-5-oxopentyl}-5-[methyl(methylsulfonyl)amino]-N'-[(1R)-1-phenylethyl]benzene-1,3-dicarboxamide
C43 H51 F2 N5 O9 S
IEIHXPJWOSDLBU-VWMOWEEZSA-N
 Ligand Interaction
SO4
Query on SO4
Download SDF File 
Download CCD File 
A, B, C
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
586Ki: <1 nM (100) BINDINGDB
586IC50: 0.3 nM (100) BINDINGDB
586IC50: 0.32 nM BINDINGMOAD
586IC50: 0.32 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.212 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 81.913α = 90.00
b = 102.705β = 103.42
c = 100.417γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
REFMACrefinement
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-03-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance