3MSJ

Structure of bace (beta secretase) in complex with inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.177 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Fragment-based discovery and optimization of BACE1 inhibitors.

Madden, J.Dod, J.R.Godemann, R.Kraemer, J.Smith, M.Biniszkiewicz, M.Hallett, D.J.Barker, J.Dyekjaer, J.D.Hesterkamp, T.

(2010) Bioorg Med Chem Lett 20: 5329-5333

  • DOI: 10.1016/j.bmcl.2010.06.089
  • Primary Citation of Related Structures:  
    3MSJ, 3MSK, 3MSL, 3S2O

  • PubMed Abstract: 
  • A novel series of 2-aminobenzimidazole inhibitors of BACE1 has been discovered using fragment-based drug discovery (FBDD) techniques. The rapid optimization of these inhibitors using structure-guided medicinal chemistry is discussed.


    Organizational Affiliation

    Evotec UK Ltd, Abingdon, UK. james.madden@evotec.com



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
BETA-SECRETASE 1A, B, C411Homo 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
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
EV3
Query on EV3

Download Ideal Coordinates CCD File 
D [auth A],
L [auth B],
U [auth C]
3-(2-amino-5-chloro-1H-benzimidazol-1-yl)propan-1-ol
C10 H12 Cl N3 O
NSMVCZCLMLZSOB-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
M [auth B],
N [auth B],
O [auth B],
P [auth B],
Q [auth B],
R [auth B],
S [auth B],
T [auth B],
V [auth C],
W [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
EV3 PDBBind:  3MSJ IC50: 7.70e+5 (nM) from 1 assay(s)
Binding MOAD:  3MSJ IC50: 7.70e+5 (nM) from 1 assay(s)
BindingDB:  3MSJ IC50: 7.70e+5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.177 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 229.196α = 90
b = 98.829β = 103.36
c = 63.132γ = 90
Software Package:
Software NamePurpose
XDSdata scaling
PHASERphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-07-14
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance