2QMF

Structure of BACE Bound to SCH735310

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.209 

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Ligand Structure Quality Assessment 


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


Literature

Potent pyrrolidine- and piperidine-based BACE-1 inhibitors.

Iserloh, U., Wu, Y., Cumming, J.N., Pan, J., Wang, L.Y., Stamford, A.W., Kennedy, M.E., Kuvelkar, R., Chen, X., Parker, E.M., Strickland, C., Voigt, J.

(2008) Bioorg Med Chem Lett 18: 414-417

  • DOI: https://doi.org/10.1016/j.bmcl.2007.10.116
  • Primary Citation of Related Structures:  
    2QK5, 2QMD, 2QMF, 2QP8

  • PubMed Abstract: 

    • Based on lead compound 1 identified from the patent literature, we developed novel patentable BACE-1 inhibitors by introducing a cyclic amine scaffold. Extensive SAR studies on both pyrrolidines and piperidines ultimately led to inhibitor 2f, one of the most potent inhibitors synthesized to date ...

    Based on lead compound 1 identified from the patent literature, we developed novel patentable BACE-1 inhibitors by introducing a cyclic amine scaffold. Extensive SAR studies on both pyrrolidines and piperidines ultimately led to inhibitor 2f, one of the most potent inhibitors synthesized to date.

    Organizational Affiliation: 

    Department of Chemical Research, Schering-Plough Research Institute, 2015 Galloping Hill Road, Kenilworth, NJ 07033, USA. ulrich.iserloh@spcorp.com



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-secretase 1
A, B
395Homo 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
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
CS9
Query on CS9
Download Ideal Coordinates CCD File 
D [auth A],
F [auth B]		N'-{(1S,2R)-1-(3,5-DIFLUOROBENZYL)-2-HYDROXY-2-[(2R,4R)-4-PHENOXYPYRROLIDIN-2-YL]ETHYL}-5-METHYL-N,N-DIPROPYLISOPHTHALAMIDE
C34 H41 F2 N3 O4
YDCNYSQITCUGST-FEFKUCBWSA-N		 Ligand Interaction
TAR
Query on TAR
Download Ideal Coordinates CCD File 
C [auth A],
E [auth B]		D(-)-TARTARIC ACID
C4 H6 O6
FEWJPZIEWOKRBE-LWMBPPNESA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
CS9 Binding MOAD:  2QMF IC50: 3 (nM) from 1 assay(s)
PDBBind:  2QMF IC50: 3 (nM) from 1 assay(s)
BindingDB:  2QMF IC50: min: 3, max: 165 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.209 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.648α = 90
b = 89.242β = 90
c = 130.962γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-03-11
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Refinement description