6X4H

Sortilin-Progranulin Interaction With Compound 24


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.204 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 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: 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 ...

    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
SortilinA663Homo 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
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseB, C2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
UOY (Subject of Investigation/LOI)
Query on UOY

Download Ideal Coordinates CCD File 
D [auth A]4-methyl-N-(6-phenoxypyridine-3-carbonyl)-L-leucine
C19 H22 N2 O4
DASSWHWKVPKLEB-HNNXBMFYSA-N
 Ligand Interaction
GOL (Subject of Investigation/LOI)
Query on GOL

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.204 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 161.458α = 90
b = 79.444β = 127
c = 111.545γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
BUSTERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

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