SMTL ID : 6x4h.1

Sortilin-Progranulin Interaction With Compound 24

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

monomer

Ligands

2 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 6 residues within 4Å: Chain A: A.270, A.271, N.272, N.321, T.323, Y.329 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 9 residues within 4Å: Chain A: E.63, D.64, Y.65, K.67, S.495, M.496, N.497, D.518, R.570 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:D.64

1 x UOY: 4-methyl-N-(6-phenoxypyridine-3-carbonyl)-L-leucine(Non-covalent)

UOY.3: 16 residues within 4Å: Chain A: Y.219, S.220, F.221, G.222, F.229, S.231, R.240, I.242, F.265, Y.266, S.267, Y.310, T.311, T.312, G.314, G.315 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:F.229, A:I.242, A:F.265, A:F.265, A:Y.266, A:Y.310 Hydrogen bonds: A:S.231, A:Y.266, A:Y.266, A:Y.266 Salt bridges: A:R.240 pi-Stacking: A:F.265

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 4 residues within 4Å: Chain A: V.27, T.485, W.501, W.512 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Stachel, S.J. et al., Identification of potent inhibitors of the sortilin-progranulin interaction. Bioorg.Med.Chem.Lett. (2020)

Release Date

2020-08-12

Peptides

Sortilin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Sortilin

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