3CKP

Crystal structure of BACE-1 in complex with inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.304 
  • R-Value Work: 0.245 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Synthesis, SAR, and X-ray structure of human BACE-1 inhibitors with cyclic urea derivatives

Park, H.Min, K.Kwak, H.-S.Koo, K.D.Lim, D.Seo, S.-W.Choi, J.-U.Platt, B.Choi, D.-Y.

(2008) Bioorg.Med.Chem.Lett. 18: 2900-2904

  • DOI: 10.1016/j.bmcl.2008.03.081
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • We describe synthesis and evaluation of a series of cyclic urea derivatives with hydroxylethylamine isostere. Modification of P3, P1, and P2' and combination of SAR display a >100-fold increase in potency with good cellular activity (IC(50)=0.15micro ...

    We describe synthesis and evaluation of a series of cyclic urea derivatives with hydroxylethylamine isostere. Modification of P3, P1, and P2' and combination of SAR display a >100-fold increase in potency with good cellular activity (IC(50)=0.15microM) relative to the previously reported compound 3.


    Organizational Affiliation

    Drug Discovery, Research & Development, LG Life Sciences, 104-1 Munji-dong, Yuseong-gu, Daejon 305-380, Republic of Korea. renivie@lgls.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-secretase 1
A, B, C
412Homo sapiensMutation(s): 2 
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
012
Query on 012

Download SDF File 
Download CCD File 
A, B, C
(4S)-N-[(1S,2R)-1-benzyl-3-{[3-(dimethylamino)benzyl]amino}-2-hydroxypropyl]-1-(3-methoxybenzyl)-2-oxoimidazolidine-4-carboxamide
(S)-1-(3-methoxy-benzyl)-2-oxo-imidazolidine-4-carboxylic acid[(1S,2R)-1-benzyl-3-(3-dimethylamino-benzylamino)-2-hydroxy-propyl]-amide
C31 H39 N5 O4
MCBWJRZWLSXSBN-YTCPBCGMSA-N
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A, B, C
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
012IC50: 14220 nM (99) BINDINGDB
012Ki: 449 nM (99) BINDINGDB
012Ki: 5001 nM BINDINGMOAD
12Ki: 449 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.304 
  • R-Value Work: 0.245 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 224.064α = 90.00
b = 105.654β = 101.47
c = 63.700γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
PDB_EXTRACTdata extraction
DENZOdata reduction
AMoREphasing
CNSrefinement
HKL-2000data scaling
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2008-03-16 
  • Released Date: 2008-06-03 
  • Deposition Author(s): Min, K.

Revision History 

  • Version 1.0: 2008-06-03
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-10-25
    Type: Refinement description