2IS0

Crystal structure of human Beta-secretase complexed with inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.235 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Discovery of oxadiazoyl tertiary carbinamine inhibitors of beta-secretase (BACE-1).

Rajapakse, H.A.Nantermet, P.G.Selnick, H.G.Munshi, S.McGaughey, G.B.Lindsley, S.R.Young, M.B.Lai, M.T.Espeseth, A.S.Shi, X.P.Colussi, D.Pietrak, B.Crouthamel, M.C.Tugusheva, K.Huang, Q.Xu, M.Simon, A.J.Kuo, L.Hazuda, D.J.Graham, S.Vacca, J.P.

(2006) J Med Chem 49: 7270-7273

  • DOI: 10.1021/jm061046r
  • Primary Citation of Related Structures:  
    2IRZ, 2IS0

  • PubMed Abstract: 
  • We describe the discovery and optimization of tertiary carbinamine derived inhibitors of the enzyme beta-secretase (BACE-1). These novel non-transition-state-derived ligands incorporate a single primary amine to interact with the catalytic aspartates of the target enzyme ...

    We describe the discovery and optimization of tertiary carbinamine derived inhibitors of the enzyme beta-secretase (BACE-1). These novel non-transition-state-derived ligands incorporate a single primary amine to interact with the catalytic aspartates of the target enzyme. Optimization of this series provided inhibitors with intrinsic and functional potency comparable to evolved transition state isostere derived inhibitors of BACE-1.


    Organizational Affiliation

    Department of Medicinal Chemistry, Merck Research Laboratories, P.O. Box 4, West Point, Pennsylvania 19486, USA. hemaka_rajapakse@merck.com



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-secretase 1A405Homo sapiensMutation(s): 2 
Gene Names: BACE1BACEKIAA1149
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
I03 (Subject of Investigation/LOI)
Query on I03

Download Ideal Coordinates CCD File 
B [auth A](2S)-2-AMINO-2-BENZYL-3-HYDROXYPROPYL 3-({[(1R)-1-(4-FLUOROPHENYL)ETHYL]AMINO}CARBONYL)-5-[METHYL(METHYLSULFONYL)AMINO]BENZOATE
C28 H32 F N3 O6 S
JVYHUOIVVLDSHT-GDJIYFAZSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
I03 Binding MOAD:  2IS0 IC50: 200 (nM) from 1 assay(s)
PDBBind:  2IS0 IC50: 200 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.235 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.67α = 90
b = 127.91β = 90
c = 76.12γ = 90
Software Package:
Software NamePurpose
CNXrefinement
d*TREKdata reduction
d*TREKdata scaling
CNXphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

  • Deposited Date: 2006-10-16 
  • Released Date: 2006-11-14 
  • Deposition Author(s): Munshi, S.

Revision History  (Full details and data files)

  • Version 1.0: 2006-11-14
    Type: Initial release
  • Version 1.1: 2007-10-11
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2021-10-20
    Changes: Database references, Derived calculations, Structure summary