2NTR

Crystal structure of Human Bace-1 bound to inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.228 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Beta-secretase (BACE-1) inhibitors: accounting for 10s loop flexibility using rigid active sites.

McGaughey, G.B.Colussi, D.Graham, S.L.Lai, M.T.Munshi, S.K.Nantermet, P.G.Pietrak, B.Rajapakse, H.A.Selnick, H.G.Stauffer, S.R.Holloway, M.K.

(2007) Bioorg.Med.Chem.Lett. 17: 1117-1121

  • DOI: 10.1016/j.bmcl.2006.11.003

  • PubMed Abstract: 
  • BACE-1 is a flexible enzyme with experimentally determined motion in the flap region, the catalytic aspartates, and the 10s loop. Four in-house crystallographically determined complexes of tertiary carbinamine inhibitors revealed 10s loop motion in t ...

    BACE-1 is a flexible enzyme with experimentally determined motion in the flap region, the catalytic aspartates, and the 10s loop. Four in-house crystallographically determined complexes of tertiary carbinamine inhibitors revealed 10s loop motion in the S(3) pocket. These X-ray structures were used to correlate K(i) values, which span over five orders of magnitude, with the calculated interaction energy, using the Merck Molecular Force Field for a series of 19 tertiary carbinamine inhibitors.


    Organizational Affiliation

    Department of Molecular Systems, Merck Research Laboratories, PO Box 4, West Point, PA 19486, USA. georgia_mcgaughey@merck.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-secretase 1
A
405Homo sapiensMutation(s): 2 
Gene Names: BACE1 (BACE, KIAA1149)
EC: 3.4.23.46
Find proteins for P56817 (Homo sapiens)
Go to Gene View: BACE1
Go to UniProtKB:  P56817
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
L00
Query on L00

Download SDF File 
Download CCD File 
A
(2R)-2-(5-{3-chloro-6-((2-methoxyethyl){[(1S,2S)-2-methylcyclopropyl]methyl}amino)-2-[methyl(methylsulfonyl)amino]pyridin-4-yl}-1,3,4-oxadiazol-2-yl)-1-phenylpropan-2-amine
N-(4-{5-[(1R)-1-AMINO-1-METHYL-2-PHENYLETHYL]-1,3,4-OXADIAZOL-2-YL}-3-CHLORO-6-[(2-METHOXYETHYL){[(1S,2S)-2-METHYLCYCLOPROPYL]METHYL}AMINO]PYRIDIN-2-YL)-N-METHYLMETHANESULFONAMIDE
C26 H35 Cl N6 O4 S
NIFMMESJJLKLHP-BNJIMDBKSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.228 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 103.922α = 90.00
b = 128.176β = 90.00
c = 76.461γ = 90.00
Software Package:
Software NamePurpose
CNXrefinement
CNXphasing
HKL-2000data reduction
HKL-2000data collection
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2006-11-08 
  • Released Date: 2007-11-13 
  • Deposition Author(s): Munshi, S.

Revision History 

  • Version 1.0: 2007-11-13
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance