SMTL ID : 8f0r.1

Structure of VSD4-NaV1.7-NaVPas channel chimera bound to the arylsulfonamide inhibitor GNE-3565

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

monomer

Ligands

1 x NAG- NAG- BMA- BMA- BMA: beta-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-BMA-BMA.1: 8 residues within 4Å: Chain A: F.356, D.358, W.361, N.385, T.397, C.398, L.399, Q.400 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.361, A:L.399

5 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)(Post Translational Modification)

NAG.2: 2 residues within 4Å: Chain A: D.1081, N.1083 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.1083 NAG.3: 2 residues within 4Å: Chain A: H.1087, N.1089 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.1089 NAG.4: 4 residues within 4Å: Chain A: W.353, N.367, S.369 Ligands: NAG.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.367, A:S.369 NAG.5: 4 residues within 4Å: Chain A: R.360, N.363, S.366 Ligands: NAG.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.360 NAG.6: 3 residues within 4Å: Chain A: D.1068, E.1069, N.1070 No protein-ligand interaction detected (PLIP)

1 x X7W: 5-chloro-4-({(1S,2S,4S)-2-(dimethylamino)-4-[3-(trifluoromethyl)phenyl]cyclohexyl}amino)-2-fluoro-N-(pyrimidin-4-yl)benzene-1-sulfonamide(Non-covalent)

X7W.7: 14 residues within 4Å: Chain A: E.1255, Y.1258, N.1261, V.1262, I.1266, S.1299, G.1302, M.1303, A.1306, D.1307, R.1323, A.1325, R.1326, R.1329 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:V.1262 Hydrogen bonds: A:D.1307, A:R.1329, A:R.1329 Salt bridges: A:E.1255, A:D.1307 pi-Stacking: A:Y.1258

2 x PEE: 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine(Non-covalent)

PEE.8: 9 residues within 4Å: Chain A: D.1100, H.1101, N.1104, L.1110, F.1162, R.1439, A.1440, A.1444, S.1448 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:L.1110, A:F.1162, A:A.1440, A:A.1444 Hydrogen bonds: A:D.1100, A:D.1100, A:N.1104 Salt bridges: A:H.1101, A:H.1101, A:R.1439, A:R.1439, A:R.1439 PEE.9: 6 residues within 4Å: Chain A: T.415, G.417, W.418, F.420, F.424, V.777 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.420, A:F.424, A:V.777 Hydrogen bonds: A:T.415

1 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.10: 7 residues within 4Å: Chain A: S.387, G.388, P.445, W.446, L.449, F.1359, F.1362 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:P.445, A:W.446, A:W.446, A:W.446, A:F.1359, A:F.1362

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kschonsak, M. et al., Cryo-EM reveals an unprecedented binding site for Na V 1.7 inhibitors enabling rational design of potent hybrid inhibitors. Elife (2023)

Release Date

2023-04-12

Peptides

Sodium channel protein PaFPC1,Sodium channel protein type 9 subunit alpha chimera: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Membrane

We predict this structure to be a membrane protein.
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Sodium channel protein PaFPC1,Sodium channel protein type 9 subunit alpha chimera

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