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 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 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: https://doi.org/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. 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)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-secretase 1
A, B, C, D
388Homo 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
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
0GH
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
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
Binding Affinity Annotations 
IDSourceBinding Affinity
0GH 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

View Full Validation Report



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
  • Version 1.2: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description