SMTL ID : 6x48.1

Sortilin-Progranulin Interaction With Compound 17

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

monomer

Ligands

1 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN.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)

1 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.2: 8 residues within 4Å: Chain A: D.64, Y.65, K.67, S.495, M.496, N.497, D.518, R.570 No protein-ligand interaction detected (PLIP)

1 x UP4: N-(3,5-dichlorobenzene-1-carbonyl)-5,5-dimethyl-L-norleucine(Non-covalent)

UP4.3: 13 residues within 4Å: Chain A: Y.219, F.221, G.222, F.229, A.230, S.231, R.240, I.242, F.265, Y.266, S.267, Y.310, G.314 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.229, A:F.265, A:Y.266 Hydrogen bonds: A:S.231, A:Y.266, A:Y.266, A:Y.266 Salt bridges: A:R.240

1 x UNL: UNKNOWN LIGAND

UNL.4: 7 residues within 4Å: Chain A: V.27, L.29, T.485, G.486, L.487, W.501, W.512 No protein-ligand interaction detected (PLIP)

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 7 residues within 4Å: Chain A: G.407, S.408, V.409, V.417, P.418, D.419, Y.421 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:G.407, A:V.409, A:V.417, A:D.419, A:Y.421 Water bridges: A:S.361, A:E.362, A:Y.421, A:K.432

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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