SMTL ID : 4n7e.1

Crystal structure of the Vps10p domain of human sortilin/NTS3 in complex with AF38469

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 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 No protein-ligand interaction detected (PLIP)

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: 9 residues within 4Å: Chain A: D.72, Y.73, K.75, R.502, S.503, M.504, N.505, D.526, R.578 No protein-ligand interaction detected (PLIP)

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.3: 7 residues within 4Å: Chain A: V.35, L.37, T.493, G.494, L.495, W.509, W.520 1 PLIP interactions: 1 interactions with chain A Water bridges: A:L.495

1 x 2JQ: 2-[(6-methylpyridin-2-yl)carbamoyl]-5-(trifluoromethyl)benzoic acid(Non-covalent)

2JQ.4: 12 residues within 4Å: Chain A: Y.227, S.228, F.229, G.230, F.237, A.238, S.239, R.248, I.250, F.273, Y.274, Y.318 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.273, A:Y.318 Hydrogen bonds: A:S.239, A:Y.274, A:Y.274, A:Y.274 Salt bridges: A:R.248 pi-Stacking: A:F.273

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schrder, T.J. et al., The identification of AF38469: An orally bioavailable inhibitor of the VPS10P family sorting receptor Sortilin. Bioorg.Med.Chem.Lett. (2014)

Release Date

2014-01-22

Peptides

Sortilin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Sortilin

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