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 

wwPDB Validation 3D Report Full Report



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

  • 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 physicoc ...

    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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
SortilinA762Homo sapiensMutation(s): 0 
Gene Names: SORT1
Find proteins for Q99523 (Homo sapiens)
Explore Q99523 
Go to UniProtKB:  Q99523
NIH Common Fund Data Resources
PHAROS  Q99523
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChainsChain Length2D Diagram Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
B, C
2 N-Glycosylation
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
UMJ
Query on UMJ

Download CCD File 
A
1-benzyl-3-tert-butyl-1H-pyrazole-5-carboxylic acid
C15 H18 N2 O2
IJXYLILRNVOJNF-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
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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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2020-08-12
    Type: Initial release