2F3E

Crystal Structure of the Bace complex with AXQ093, a macrocyclic inhibitor

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.208 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history. 


Literature

Structure-based design and synthesis of macroheterocyclic peptidomimetic inhibitors of the aspartic protease beta-site amyloid precursor protein cleaving enzyme (BACE).

Hanessian, S., Yang, G., Rondeau, J.-M., Neumann, U., Betschart, C., Tintelnot-Blomley, M.

(2006) J Med Chem 49: 4544-4567

  • DOI: 10.1021/jm060154a
  • Primary Citation of Related Structures:  
    2F3E, 2F3F

  • PubMed Abstract: 

    • Based on the X-ray cocrystal structure of the Tang-Ghosh heptapeptide inhibitor 1 (OM00-3), a series of macroheterocyclic analogues were designed and synthesized. Analogues containing dithia, dioxa, oxathia, and carbathia macrocycles were synthesized by methods relying on ring-closing olefin metathesis for the dioxa analogues and by alkylation of thiolates or bisthiolates for the others ...

    Based on the X-ray cocrystal structure of the Tang-Ghosh heptapeptide inhibitor 1 (OM00-3), a series of macroheterocyclic analogues were designed and synthesized. Analogues containing dithia, dioxa, oxathia, and carbathia macrocycles were synthesized by methods relying on ring-closing olefin metathesis for the dioxa analogues and by alkylation of thiolates or bisthiolates for the others. Molecular modeling suggested that the incorporation of piperidine units appended to the macrocycles improved interactions through additional H-bonds and introduced further rigidity. These were synthesized in enantiomerically pure form using enzyme-catalyzed desymmetrization and diastereomer separation. Inhibitory activity on beta-site amyloid precursor protein cleaving enzyme (BACE) was observed with several macroheterocyclic inhibitors and structure-activity relationship (SAR) correlations were deduced. Cocrystal structures of two synthetic analogues revealed interesting and unexpected binding interactions.

    Organizational Affiliation: 

    Department of Chemistry, Université de Montréal, C. P. 6128, Station Centre-ville, Montréal, Quebec H3C 3J7, Canada. stephen.hanessian@umontreal.ca



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-secretase 1A, B, C402Homo 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 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AXQ
Query on AXQ
Download Ideal Coordinates CCD File 
D [auth A],
E [auth B],
F [auth C]		{(E)-(3R,6S,9R)-3-[(1S,3R)-3-((S)-1 -BUTYLCARBAMOYL-2-METHYL-PROPYLCARB AMOYL)-1-HYDROXY-BUTYL]-6-METHYL-5, 8-DIOXO-1,11-DITHIA-4,7-DIAZA-CYCLO PENTADEC-13-EN-9-YL}-CARBAMIC ACID TERT-BUTYL ESTER
C31 H55 N5 O7 S2
YFVXRNZNJJXEKV-DYASFXQMSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
AXQ PDBBind:  2F3E IC50: 156 (nM) from 1 assay(s)
BindingDB:  2F3E IC50: 156 (nM) from 1 assay(s)
Binding MOAD:  2F3E IC50: 156 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.208 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.244α = 90
b = 103.781β = 103.04
c = 100.961γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACTdata extraction
CNXphasing
CNXrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2005-11-21 
  • Released Date: 2006-09-05 
    • Deposition Author(s): Rondeau, J.-M.

Revision History  (Full details and data files)

  • Version 1.0: 2006-09-05
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description