3L5C

Structure of BACE Bound to SCH723871

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.196 

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Ligand Structure Quality Assessment 


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


Literature

Discovery of Cyclic Acylguanidines as Highly Potent and Selective beta-Site Amyloid Cleaving Enzyme (BACE) Inhibitors: Part I-Inhibitor Design and Validation

Zhu, Z., Sun, Z.Y., Ye, Y., Voigt, J., Strickland, C., Smith, E.M., Cumming, J., Wang, L., Wong, J., Wang, Y.S., Wyss, D.F., Chen, X., Kuvelkar, R., Kennedy, M.E., Favreau, L., Parker, E., McKittrick, B.A., Stamford, A., Czarniecki, M., Greenlee, W., Hunter, J.C.

(2010) J Med Chem 53: 951-965

  • DOI: 10.1021/jm901408p
  • Primary Citation of Related Structures:  
    3L58, 3L59, 3L5B, 3L5C, 3L5D, 3L5E, 3L5F

  • PubMed Abstract: 

    • A number of novel amidine containing heterocycles were designed to reproduce the unique interaction pattern, revealed by X-ray crystallography, between the BACE-1 catalytic diad and a weak NMR screening hit (3), with special attention paid to maintaining the appropriate basicity and limiting the number of H-bonding donors of these scaffolds ...

    A number of novel amidine containing heterocycles were designed to reproduce the unique interaction pattern, revealed by X-ray crystallography, between the BACE-1 catalytic diad and a weak NMR screening hit (3), with special attention paid to maintaining the appropriate basicity and limiting the number of H-bonding donors of these scaffolds. The iminohydantoin cores (10 and 23) were examined first and found to interact with the catalytic diad in one of two binding modes (A and B), each with the iminohydantoin core flipped 180 degrees in relation to the other. The amidine structural motif within each core forms a bidentate interaction with a different aspartic acid of the catalytic diad. Both modes reproduced a highly conserved interaction pattern between the inhibitors and the catalytic aspartates, as revealed by 3. Potent iminohydantoin BACE-1 inhibitors have been obtained, validating the molecular design as aspartyl protease catalytic site inhibitors. Brain penetrant small molecule BACE inhibitors with high ligand efficiencies have been discovered, enabling multiple strategies for further development of these inhibitors into highly potent, selective and in vivo efficacious BACE inhibitors.

    Organizational Affiliation: 

    Department of Medicinal Chemistry, Schering-Plough Research Institute, 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, USA. Zhaoning.Zhu@spcorp.com



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-secretase 1A, B414Homo 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
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
BDQ
Query on BDQ
Download Ideal Coordinates CCD File 
D [auth A],
F [auth B]		1-(4-cyanophenyl)-3-(4-{[(2Z,4R)-2-imino-4-methyl-4-(2-methylpropyl)-5-oxoimidazolidin-1-yl]methyl}benzyl)urea
C24 H28 N6 O2
CTKHUQYUPSHMQE-XMMPIXPASA-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
BDQ PDBBind:  3L5C IC50: 7000 (nM) from 1 assay(s)
Binding MOAD:  3L5C IC50: 7000 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.196 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.261α = 90
b = 89.334β = 90
c = 130.836γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
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: 2010-02-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Refinement description