3L38 | pdb_00003l38

Bace1 in complex with the aminopyridine Compound 44


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.246 (Depositor), 0.239 (DCC) 
  • R-Value Work: 
    0.211 (Depositor), 0.206 (DCC) 
  • R-Value Observed: 
    0.213 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 3L38

Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Novel pyrrolyl 2-aminopyridines as potent and selective human beta-secretase (BACE1) inhibitors.

Malamas, M.S.Barnes, K.Hui, Y.Johnson, M.Lovering, F.Condon, J.Fobare, W.Solvibile, W.Turner, J.Hu, Y.Manas, E.S.Fan, K.Olland, A.Chopra, R.Bard, J.Pangalos, M.N.Reinhart, P.Robichaud, A.J.

(2010) Bioorg Med Chem Lett 20: 2068-2073

  • DOI: https://doi.org/10.1016/j.bmcl.2010.02.075
  • Primary Citation Related Structures: 
    3L38, 3L3A

  • PubMed Abstract: 

    The proteolytic enzyme beta-secretase (BACE1) plays a central role in the synthesis of the pathogenic beta-amyloid in Alzheimer's disease. Recently, we reported small molecule acylguanidines as potent BACE1 inhibitors. However, many of these acylguanidines have a high polar surface area (e.g. as measured by the topological polar surface area or TPSA), which is unfavorable for crossing the blood-brain barrier. Herein, we describe the identification of the 2-aminopyridine moiety as a bioisosteric replacement of the acylguanidine moiety, which resulted in inhibitors with lower TPSA values and superior brain penetration. X-ray crystallographic studies indicated that the 2-aminopyridine moiety interacts directly with the catalytic aspartic acids Asp32 and Asp228 via a hydrogen-bonding network.


  • Organizational Affiliation
    • Department of Chemical Sciences, Wyeth, CN 8000, Princeton, NJ 08543-8000, USA. malamas.michael@gmail.com

Macromolecule Content 

  • Total Structure Weight: 46.89 kDa 
  • Atom Count: 3,011 
  • Modeled Residue Count: 364 
  • Deposited Residue Count: 415 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Beta-secretase 1415Homo sapiensMutation(s): 0 
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
GTEx:  ENSG00000186318 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP56817
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
879

Query on 879



Download:Ideal Coordinates CCD File
B [auth A]6-({2-(2-chlorophenyl)-5-[4-(pyrimidin-5-yloxy)phenyl]-1H-pyrrol-1-yl}methyl)pyridin-2-amine
C26 H20 Cl N5 O
MNZJYJDKCYJKMU-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.246 (Depositor), 0.239 (DCC) 
  • R-Value Work:  0.211 (Depositor), 0.206 (DCC) 
  • R-Value Observed: 0.213 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.253α = 90
b = 103.687β = 95.04
c = 49.983γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
AMoREphasing
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-04-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.3: 2024-10-09
    Changes: Structure summary