SMTL ID : 8f0s.1

Structure of VSD4-NaV1.7-NaVPas channel chimera bound to the hybrid inhibitor GNE-9296

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-mer

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 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.399

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG-NAG.2: 2 residues within 4Å: Chain A: N.363 Ligands: NAG.5 No protein-ligand interaction detected (PLIP)

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

NAG.3: 2 residues within 4Å: Chain A: N.1089 Chain B: Y.47 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.1089 NAG.4: 2 residues within 4Å: Chain A: E.1069, N.1070 No protein-ligand interaction detected (PLIP) NAG.5: 3 residues within 4Å: Chain A: N.367, S.369 Ligands: NAG-NAG.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.367, A:S.369 NAG.6: 2 residues within 4Å: Chain A: N.1083, D.1084 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.1083, A:D.1084

1 x X80: 5-chloro-4-(cyclopentylmethoxy)-N-(4-{[(1S,2S)-2-(dimethylamino)cyclohexyl]amino}-2-fluorobenzene-1-sulfonyl)-2-fluorobenzamide(Non-covalent)

X80.7: 15 residues within 4Å: Chain A: Y.1258, W.1259, N.1261, I.1265, I.1298, S.1299, G.1302, M.1303, A.1306, D.1307, I.1322, R.1323, A.1325, R.1326, R.1329 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:Y.1258, A:Y.1258, A:I.1298, A:A.1306, A:D.1307, A:I.1322 Hydrogen bonds: A:R.1323, A:R.1326, A:R.1329, A:R.1329 Halogen bonds: A:R.1329

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

PEE.8: 9 residues within 4Å: Chain A: N.385, S.386, S.387, W.446, H.447, T.1317, V.1321, L.1324, G.1328 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:W.446, A:V.1321, A:L.1324 Hydrogen bonds: A:S.387, A:S.1315, A:S.1315 Salt bridges: A:H.447

1 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.9: 12 residues within 4Å: Chain A: S.387, G.388, P.445, W.446, I.448, L.449, I.452, S.1358, F.1359, F.1362, G.1395, I.1398 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:P.445, A:W.446, A:W.446, A:I.448, A:I.452, A:F.1359, A:F.1362, A:I.1398

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
Beta-diguetoxin-Dc1a: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

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

Beta-diguetoxin-Dc1a

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