4N7E

Crystal structure of the Vps10p domain of human sortilin/NTS3 in complex with AF38469


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.201 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

The identification of AF38469: An orally bioavailable inhibitor of the VPS10P family sorting receptor Sortilin.

Schrder, T.J.Christensen, S.Lindberg, S.Langgard, M.David, L.Maltas, P.J.Eskildsen, J.Jacobsen, J.Tagmose, L.Simonsen, K.B.Biilmann Rnn, L.C.de Jong, I.E.Malik, I.J.Karlsson, J.J.Bundgaard, C.Egebjerg, J.Stavenhagen, J.B.Strandbygard, D.Thirup, S.Andersen, J.L.Uppalanchi, S.Pervaram, S.Kasturi, S.P.Eradi, P.Sakumudi, D.R.Watson, S.P.

(2014) Bioorg.Med.Chem.Lett. 24: 177-180

  • DOI: 10.1016/j.bmcl.2013.11.046

  • PubMed Abstract: 
  • The identification of the novel, selective, orally bioavailable Sortilin inhibitor AF38469 is described. Structure-activity relationships and syntheses are reported, along with an X-ray crystal structure of the sortilin-AF38469 protein-inhibitor comp ...

    The identification of the novel, selective, orally bioavailable Sortilin inhibitor AF38469 is described. Structure-activity relationships and syntheses are reported, along with an X-ray crystal structure of the sortilin-AF38469 protein-inhibitor complex.


    Organizational Affiliation

    Neuroscience Drug Discovery, H. Lundbeck A/S, Copenhagen, 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 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BMA
Query on BMA

Download SDF File 
Download CCD File 
A
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-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
2JQ
Query on 2JQ

Download SDF File 
Download CCD File 
A
2-[(6-methylpyridin-2-yl)carbamoyl]-5-(trifluoromethyl)benzoic acid
C15 H11 F3 N2 O3
JWCUSQCZMQIBMR-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
2JQIC50: 260 - 1800 nM (99) BINDINGDB
2JQKi: 429 nM (99) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.201 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 161.948α = 90.00
b = 77.402β = 127.06
c = 111.176γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
SCALAdata scaling
PHASERphasing
DNAdata collection
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-01-22
    Type: Initial release