SMTL ID : 5mri.1

Crystal structure of the Vps10p domain of human sortilin/NTS3 in complex with Triazolone 18

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

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.1: 6 residues within 4Å: Chain A: A.278, A.279, N.280, N.329, T.331, Y.337 3 PLIP interactions: 3 interactions with chain A Water bridges: A:N.280, A:N.280, A:D.281

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

NAG-NAG.2: 10 residues within 4Å: Chain A: D.72, Y.73, K.75, R.502, S.503, M.504, N.505, D.526, Q.575, R.578 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:D.72

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

NAG.3: 5 residues within 4Å: Chain A: L.83, N.85, F.121, F.130, Q.132 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.121, A:Q.132 Hydrogen bonds: A:Q.132 Water bridges: A:Q.132

1 x Q9Y: ~{N}-methyl-3-(3-methylbutyl)-5-oxidanyl-1,2,3-triazole-4-carboxamide(Non-covalent)

Q9Y.4: 10 residues within 4Å: Chain A: S.228, F.229, G.230, F.237, A.238, S.239, R.248, I.250, F.273, Y.274 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.237, A:I.250 Hydrogen bonds: A:S.239, A:R.248, A:Y.274, A:Y.274 Water bridges: A:S.228, A:I.276

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Andersen, J.L. et al., The identification of novel acid isostere based inhibitors of the VPS10P family sorting receptor Sortilin. Bioorg. Med. Chem. Lett. (2017)

Release Date

2017-05-17

Peptides

Sortilin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Sortilin

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