5MRH

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

• PDB DOI: https://doi.org/10.2210/pdb5MRH/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2016-12-23 Released: 2017-05-17 
• Deposition Author(s): Andersen, J.L., Strandbygaard, D., Thirup, S.
• Funding Organization(s): DanScatt: the Danish Centre for the Use of Synchrotron X-ray and Neutron Facilities, Biostruct-X

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.233 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.211 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.212 (Depositor) 

Starting Model: experimental

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

• PubMed: 28462834 
• DOI: https://doi.org/10.1016/j.bmcl.2017.02.028
• Primary Citation of Related Structures:  
  5MRH, 5MRI


• 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 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.

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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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 78.95 kDa 
• Atom Count: 5,157 
• Modelled Residue Count: 639 
• Deposited Residue Count: 696 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sortilin	A	696	Homo sapiens	Mutation(s): 0  Gene Names: SORT1
UniProt & NIH Common Fund Data Resources
Find proteins for Q99523 (Homo sapiens) Explore Q99523  Go to UniProtKB:  Q99523
PHAROS:  Q99523 GTEx:  ENSG00000134243
Glycosylation
Glycosylation Sites: 2		Go to GlyGen: Q99523-1

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B, C	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
Q9Z	D [auth A]	3-(3-methylbutyl)-4~{H}-1,2,3-triazol-5-one C7 H13 N3 O NRFSJPLMHMLGTM-UHFFFAOYSA-N
PGE	E [auth A]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
Q9Z	BindingDB:  5MRH	IC50: 6.31e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.233 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.211 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.212 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 162.395	α = 90
b = 78.23	β = 127.2
c = 111.796	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-05-17 
Deposition Author(s): Andersen, J.L., Strandbygaard, D., Thirup, S.

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Funding Organization	Location	Grant Number
DanScatt: the Danish Centre for the Use of Synchrotron X-ray and Neutron Facilities	Denmark	--
Biostruct-X	Denmark	283570

Revision History  

• Version 1.0: 2017-05-17
  Type: Initial release
  
• Version 1.1: 2017-08-09
  Changes: Data collection, Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2024-01-17
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 2.2: 2024-11-13
  Changes: Structure summary