4GID

Structure of beta-secretase complexed with inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.216 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Structure-based design of highly selective beta-secretase inhibitors: synthesis, biological evaluation, and protein-ligand X-ray crystal structure.

Ghosh, A.K.Venkateswara Rao, K.Yadav, N.D.Anderson, D.D.Gavande, N.Huang, X.Terzyan, S.Tang, J.

(2012) J Med Chem 55: 9195-9207

  • DOI: 10.1021/jm3008823
  • Primary Citation of Related Structures:  
    4GID

  • PubMed Abstract: 
  • The structure-based design, synthesis, and X-ray structure of protein-ligand complexes of exceptionally potent and selective β-secretase inhibitors are described. The inhibitors are designed specifically to interact with S(1)' active site residues to provide selectivity over memapsin 1 and cathepsin D ...

    The structure-based design, synthesis, and X-ray structure of protein-ligand complexes of exceptionally potent and selective β-secretase inhibitors are described. The inhibitors are designed specifically to interact with S(1)' active site residues to provide selectivity over memapsin 1 and cathepsin D. Inhibitor 5 has exhibited exceedingly potent inhibitory activity (K(i) = 17 pM) and high selectivity over BACE 2 (>7000-fold) and cathepsin D (>250000-fold). A protein-ligand crystal structure revealed important molecular insight into these selectivities. These interactions may serve as an important guide to design selectivity over the physiologically important aspartic acid proteases.


    Organizational Affiliation

    Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States. akghosh@purdue.edu



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-secretase 1A, B, C, D388Homo 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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0GH (Subject of Investigation/LOI)
Query on 0GH

Download Ideal Coordinates CCD File 
E [auth A], G [auth B], I [auth C], K [auth D]N-[(2S)-1-({(2S,3R)-3-hydroxy-1-[(2-methylpropyl)amino]-1-oxobutan-2-yl}amino)-3-phenylpropan-2-yl]-5-[methyl(methylsulfonyl)amino]-N'-[(1R)-1-phenylethyl]benzene-1,3-dicarboxamide
C35 H47 N5 O6 S
UZFAOTIMARRSKT-TYUOOWEOSA-N
 Ligand Interaction
LPD
Query on LPD

Download Ideal Coordinates CCD File 
F [auth A], H [auth B], J [auth C], L [auth D]L-PROLINAMIDE
C5 H10 N2 O
VLJNHYLEOZPXFW-BYPYZUCNSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
0GH BindingDB:  4GID Ki: 99 (nM) from 1 assay(s)
IC50: 1000 (nM) from 1 assay(s)
Binding MOAD:  4GID Ki: 0.02 (nM) from 1 assay(s)
PDBBind:  4GID Ki: 0.02 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.216 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.427α = 90
b = 130.353β = 97.5
c = 88.401γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-10-10
    Type: Initial release
  • Version 1.1: 2013-08-28
    Changes: Database references