5MRH

Crystal structure of the Vps10p domain of human sortilin/NTS3 in complex with Triazolone 1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.211 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The identification of novel acid isostere based inhibitors of the VPS10P family sorting receptor Sortilin.

Andersen, J.L.Lindberg, S.Langgard, M.Maltas, P.J.Ronn, L.C.B.Bundgaard, C.Strandbygaard, D.Thirup, S.Watson, S.P.

(2017) Bioorg. Med. Chem. Lett. 27: 2629-2633

  • DOI: 10.1016/j.bmcl.2017.02.028
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Using fragment based and structure based drug discovery strategies a series of novel Sortilin inhibitors has been identified. The inhibitors are based on the N-substituted 1,2,3-triazol-4-one/ol heterocyclic template. X-ray crystallography shows that ...

    Using fragment based and structure based drug discovery strategies a series of novel Sortilin inhibitors has been identified. The inhibitors are based on the N-substituted 1,2,3-triazol-4-one/ol heterocyclic template. X-ray crystallography shows that the 1,2,3-triazol-4-one/ol acts as a carboxylic acid isostere, making a bi-dentate interaction with an arginine residue of Sortilin, an interaction which has not been previously characterised for this heterocycle.


    Organizational Affiliation

    The Lundbeck Foundation Research Centre MIND, Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10C, Aarhus C 8000, Denmark; Department of Biomedicine, Aarhus University, Ole Worms Allé 3, Aarhus C 8000, Denmark.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Sortilin
A
696Homo sapiensMutation(s): 0 
Gene Names: SORT1
Find proteins for Q99523 (Homo sapiens)
Go to Gene View: SORT1
Go to UniProtKB:  Q99523
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
Q9Z
Query on Q9Z

Download SDF File 
Download CCD File 
A
3-(3-methylbutyl)-4~{H}-1,2,3-triazol-5-one
C7 H13 N3 O
NRFSJPLMHMLGTM-UHFFFAOYSA-N
 Ligand Interaction
PGE
Query on PGE

Download SDF File 
Download CCD File 
A
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
Q9ZIC50: 63100 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.211 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 162.395α = 90.00
b = 78.230β = 127.20
c = 111.796γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
PHASERphasing
XDSdata reduction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
DanScatt: the Danish Centre for the Use of Synchrotron X-ray and Neutron FacilitiesDenmark--
Biostruct-XDenmark283570

Revision History 

  • Version 1.0: 2017-05-17
    Type: Initial release
  • Version 1.1: 2017-08-09
    Type: Data collection, Database references