6X3L

Sortilin-Progranulin Interaction With Compound 2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.219 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Identification of potent inhibitors of the sortilin-progranulin interaction.

Stachel, S.J.Ginnetti, A.T.Johnson, S.A.Cramer, P.Wang, Y.Bukhtiyarova, M.Krosky, D.Stump, C.Hurzy, D.M.Schlegel, K.A.Cooke, A.J.Allen, S.O'Donnell, G.Ziebell, M.Parthasarathy, G.Getty, K.L.Ho, T.Ou, Y.Jovanovska, A.Carroll, S.S.Pausch, M.Lumb, K.Mosser, S.D.Voleti, B.Klein, D.J.Soisson, S.M.Zerbinatti, C.Coleman, P.J.

(2020) Bioorg Med Chem Lett 30: 127403-127403

  • DOI: https://doi.org/10.1016/j.bmcl.2020.127403
  • Primary Citation of Related Structures:  
    6X3L, 6X48, 6X4H

  • PubMed Abstract: 

    High-throughput screening methods have been used to identify two novel series of inhibitors that disrupt progranulin binding to sortilin. Exploration of structure-activity relationships (SAR) resulted in compounds with sufficient potency and physicochemical properties to enable co-crystallization with sortilin. These co-crystal structures supported observed SAR trends and provided guidance for additional avenues for designing compounds with additional interactions within the binding site.


  • Organizational Affiliation

    Department of Medicinal Chemistry, Merck & Co. Inc., PO Box 4, West Point, PA 19486, USA. Electronic address: shawn_stachel@merck.com.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Sortilin762Homo sapiensMutation(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 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ99523
Glycosylation
Glycosylation Sites: 2Go to GlyGen: Q99523-1
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
B, C
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
UMJ (Subject of Investigation/LOI)
Query on UMJ

Download Ideal Coordinates CCD File 
D [auth A]1-benzyl-3-tert-butyl-1H-pyrazole-5-carboxylic acid
C15 H18 N2 O2
IJXYLILRNVOJNF-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
E [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.219 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 161.832α = 90
b = 75.513β = 127.01
c = 110.984γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
PDB_EXTRACTdata extraction
HKL-3000data reduction
HKL-3000data scaling
BUSTERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-08-12
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Database references, Refinement description
  • Version 1.2: 2024-10-23
    Changes: Structure summary