3CKR

Crystal structure of BACE-1 in complex with inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.251 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 009Click on this verticalbar to view details

This is version 1.4 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: https://doi.org/10.1016/j.bmcl.2008.03.081
  • Primary Citation of Related Structures:  
    3CKP, 3CKR

  • 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)=0.15microM) 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-secretase 1
A, B, C
412Homo sapiensMutation(s): 2 
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
GTEx:  ENSG00000186318 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP56817
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
009 BindingDB:  3CKR Ki: 5001 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.251 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 224.457α = 90
b = 108.126β = 100.87
c = 61.135γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 009Click on this verticalbar to view details

Entry History 

Deposition Data

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

Revision History  (Full details and data files)

  • Version 1.0: 2008-06-03
    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: 2021-11-10
    Changes: Database references, Derived calculations
  • Version 1.4: 2024-11-13
    Changes: Data collection, Structure summary