2G94

Crystal structure of beta-secretase bound to a potent and highly selective inhibitor.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.199 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Design, synthesis and X-ray structure of protein-ligand complexes: important insight into selectivity of memapsin 2 (beta-secretase) inhibitors.

Ghosh, A.K., Kumaragurubaran, N., Hong, L., Lei, H., Hussain, K.A., Liu, C.F., Devasamudram, T., Weerasena, V., Turner, R., Koelsch, G., Bilcer, G., Tang, J.

(2006) J Am Chem Soc 128: 5310-5311

  • DOI: 10.1021/ja058636j
  • Primary Citation of Related Structures:  
    2G94

  • PubMed Abstract: 

    • Structure-based design, synthesis, and X-ray structure of protein-ligand complexes of memapsin 2 are described. The inhibitors are designed specifically to interact with S2- and S3-active site residues to provide selectivity over memapsin 1 and cathepsin D ...

    Structure-based design, synthesis, and X-ray structure of protein-ligand complexes of memapsin 2 are described. The inhibitors are designed specifically to interact with S2- and S3-active site residues to provide selectivity over memapsin 1 and cathepsin D. Inhibitor 6 has exhibited exceedingly potent inhibitory activity against memapsin 2 and selectivity over memapsin 1 (>3800-fold) and cathepsin D (>2500-fold). A protein-ligand crystal structure revealed cooperative interactions in the S2- and S3-active sites of memapsin 2. These interactions may serve as an important guide to design selectivity over memapsin 1 and cathepsin D.

    Organizational Affiliation: 

    Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, USA. akghosh@purdue.edu



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-secretase 1A, B, C, D389Homo sapiensMutation(s): 0 
Gene Names: BACE1, BACE, KIAA1149
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
ZPQ
Query on ZPQ
Download Ideal Coordinates CCD File 
E [auth A],
F [auth B],
G [auth C],
H [auth D]		N~2~-[(2R,4S,5S)-5-{[N-{[(3,5-DIMETHYL-1H-PYRAZOL-1-YL)METHOXY]CARBONYL}-3-(METHYLSULFONYL)-L-ALANYL]AMINO}-4-HYDROXY-2,7-DIMETHYLOCTANOYL]-N-ISOBUTYL-L-VALINAMIDE
C30 H54 N6 O8 S
OFAZWNGNAATRSH-GWCXRDAXSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
ZPQ PDBBind:  2G94 Ki: 0.3 (nM) from 1 assay(s)
BindingDB:  2G94 Ki: 0.3 (nM) from 1 assay(s)
Binding MOAD:  2G94 Ki: 0.3 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.199 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.628α = 90
b = 131.024β = 97.39
c = 88.236γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing

Structure Validation

View Full Validation Report



View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-04-25
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance