3OHH

Crystal structure of beta-site app-cleaving enzyme 1 (bace-wt) complex with bms-681889 aka n~1~-butyl-5-cyano- n~3~-((1s,2r)-1-(3,5-difluorobenzyl)-2-hydroxy-3-((3- methoxybenzyl)amino)propyl)-n~1~-methyl-1h-indole-1,3- dicarboxamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.171 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Synthesis and SAR of indole-and 7-azaindole-1,3-dicarboxamide hydroxyethylamine inhibitors of BACE-1.

Marcin, L.R.Higgins, M.A.Zusi, F.C.Zhang, Y.Dee, M.F.Parker, M.F.Muckelbauer, J.K.Camac, D.M.Morin, P.E.Ramamurthy, V.Tebben, A.J.Lentz, K.A.Grace, J.E.Marcinkeviciene, J.A.Kopcho, L.M.Burton, C.R.Barten, D.M.Toyn, J.H.Meredith, J.E.Albright, C.F.Bronson, J.J.Macor, J.E.Thompson, L.A.

(2011) Bioorg.Med.Chem.Lett. 21: 537-541

  • DOI: 10.1016/j.bmcl.2010.10.079
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Heterocyclic replacement of the isophthalamide phenyl ring in hydroxyethylamine (HEA) BACE-1 inhibitors was explored. A variety of indole-1,3-dicarboxamide HEAs exhibited potent BACE-1 enzyme inhibition, but displayed poor cellular activity. Improvem ...

    Heterocyclic replacement of the isophthalamide phenyl ring in hydroxyethylamine (HEA) BACE-1 inhibitors was explored. A variety of indole-1,3-dicarboxamide HEAs exhibited potent BACE-1 enzyme inhibition, but displayed poor cellular activity. Improvements in cellular activity and aspartic protease selectivity were observed for 7-azaindole-1,3-dicarboxamide HEAs. A methylprolinol-bearing derivative (10n) demonstrated robust reductions in rat plasma Aβ levels, but did not lower rat brain Aβ due to poor central exposure. The same analog exhibited a high efflux ratio in a bidirectional Caco-2 assay and was likely a substrate of the efflux transporter P-glycoprotein. X-ray crystal structures are reported for two indole HEAs in complex with BACE-1.


    Organizational Affiliation

    Bristol-Myers Squibb, Research and Development, 5 Research Parkway, Wallingford, CT 06492-7660, USA. lawrence.marcin@bms.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-secretase 1
A, B
455Homo 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 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
3HH
Query on 3HH

Download SDF File 
Download CCD File 
A, B
N~1~-butyl-5-cyano-N~3~-{(1S,2R)-1-(3,5-difluorobenzyl)-2-hydroxy-3-[(3-methoxybenzyl)amino]propyl}-N~1~-methyl-1H-indole-1,3-dicarboxamide
C34 H37 F2 N5 O4
ZAVRTXWWDAGODB-XDFJSJKPSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
3HHIC50: 18 nM BINDINGMOAD
3HHIC50: 18 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.171 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 92.177α = 90.00
b = 86.551β = 100.45
c = 130.448γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
DENZOdata reduction
REFMACrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2010-08-17 
  • Released Date: 2011-04-06 
  • Deposition Author(s): Muckelbauer, J.K.

Revision History 

  • Version 1.0: 2011-04-06
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-03-01
    Type: Database references
  • Version 1.3: 2017-11-08
    Type: Refinement description