3LPJ

Structure of BACE Bound to SCH743641

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.179 

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Ligand Structure Quality Assessment 


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


Literature

Piperazine sulfonamide BACE1 inhibitors: design, synthesis, and in vivo characterization.

Cumming, J., Babu, S., Huang, Y., Carrol, C., Chen, X., Favreau, L., Greenlee, W., Guo, T., Kennedy, M., Kuvelkar, R., Le, T., Li, G., McHugh, N., Orth, P., Ozgur, L., Parker, E., Saionz, K., Stamford, A., Strickland, C., Tadesse, D., Voigt, J., Zhang, L., Zhang, Q.

(2010) Bioorg Med Chem Lett 20: 2837-2842

  • DOI: 10.1016/j.bmcl.2010.03.050
  • Primary Citation of Related Structures:  
    3LNK, 3LPI, 3LPJ, 3LPK

  • PubMed Abstract: 

    • With collaboration between chemistry, X-ray crystallography, and molecular modeling, we designed and synthesized a series of novel piperazine sulfonamide BACE1 inhibitors. Iterative exploration of the non-prime side and S2' sub-pocket of the enzyme culminated in identification of an analog that potently lowers peripheral Abeta(40) in transgenic mice with a single subcutaneous dose ...

    With collaboration between chemistry, X-ray crystallography, and molecular modeling, we designed and synthesized a series of novel piperazine sulfonamide BACE1 inhibitors. Iterative exploration of the non-prime side and S2' sub-pocket of the enzyme culminated in identification of an analog that potently lowers peripheral Abeta(40) in transgenic mice with a single subcutaneous dose.

    Organizational Affiliation: 

    Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, NJ 07033, USA. jared.cumming@merck.com



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-secretase 1A, B455Homo sapiensMutation(s): 0 
Gene Names: BACE, BACE1, 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
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
Z75
Query on Z75
Download Ideal Coordinates CCD File 
D [auth A],
F [auth B]		N'-[(1S,2S)-2-[(2R)-4-benzylpiperazin-2-yl]-1-(3,5-difluorobenzyl)-2-hydroxyethyl]-5-methyl-N,N-dipropylbenzene-1,3-dicarboxamide
C35 H44 F2 N4 O3
ZHZSBUKNHGZRTJ-DSPMFFIESA-N		 Ligand Interaction
TLA
Query on TLA
Download Ideal Coordinates CCD File 
C [auth A],
E [auth B]		L(+)-TARTARIC ACID
C4 H6 O6
FEWJPZIEWOKRBE-JCYAYHJZSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
Z75 BindingDB:  3LPJ IC50: 120 (nM) from 1 assay(s)
PDBBind:  3LPJ IC50: 120 (nM) from 1 assay(s)
Binding MOAD:  3LPJ IC50: 120 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.179 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.333α = 90
b = 89.046β = 90
c = 130.889γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling
CNXphasing
CNXrefinement

Structure Validation

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Ligand Structure Quality Assessment 


View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-04-14
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Refinement description