5DQC

Co-crystal of BACE1 with compound 0211


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.47 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Design of Potent and Highly Selective Inhibitors for Human beta-Secretase 2 (Memapsin 1), a Target for Type 2 Diabetes.

Ghosh, A.K.Reddy, B.S.Yen, Y.C.Cardenas, E.Rao, K.V.Downs, D.Huang, X.Tang, J.Mesecar, A.D.

(2016) Chem Sci 7: 3117-3122

  • DOI: 10.1039/C5SC03718B
  • Primary Citation of Related Structures:  
    5DQC

  • PubMed Abstract: 
  • Design, synthesis and evaluation of very potent and selective β-Secretase 2 (memapsin 1, BACE 2) inhibitors are described. The inhibitors were designed specifically to interact with the S2'-site of β-secretase 2 to provide >170,000-fold selectivity over β-secretase (BACE 1) and >15,000-fold selectivity over cathepsin D ...

    Design, synthesis and evaluation of very potent and selective β-Secretase 2 (memapsin 1, BACE 2) inhibitors are described. The inhibitors were designed specifically to interact with the S2'-site of β-secretase 2 to provide >170,000-fold selectivity over β-secretase (BACE 1) and >15,000-fold selectivity over cathepsin D. BACE 2 is implicated in Type 2 diabetes. The studies serve as an important guide to selective BACE 2 inhibitors.


    Organizational Affiliation

    Department of Biological Sciences, Purdue University, West Lafayette, IN 47907 (USA); Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907 (USA); Department of Biochemistry, Purdue University, West Lafayette, IN 47907 (USA).



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-secretase 1A, B, C390Homo sapiensMutation(s): 0 
Gene Names: BACE1BACEKIAA1149
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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
5E7
Query on 5E7

Download Ideal Coordinates CCD File 
D [auth A],
E [auth B],
F [auth C]
N-[(2S,3R)-3-hydroxy-4-({(2S,3S)-3-hydroxy-1-[(2-methylpropyl)amino]-1-oxobutan-2-yl}amino)-1-phenylbutan-2-yl]-5-[methyl(methylsulfonyl)amino]-N'-[(1R)-1-phenylethyl]benzene-1,3-dicarboxamide
C36 H49 N5 O7 S
ZIEVAMMZKBNDFB-AAZBAGLXSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
5E7 Binding MOAD:  5DQC Ki: 45.6 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.47 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.95α = 90
b = 103.403β = 102.66
c = 100.834γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-02-17
    Type: Initial release
  • Version 1.1: 2016-07-13
    Changes: Database references