SMTL ID : 8f0p.1

Structure of VSD4-NaV1.7-NaVPas channel chimera bound to the hybrid inhibitor GNE-1305

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 No protein-ligand interaction detected (PLIP)

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

NAG.2: 2 residues within 4Å: Chain A: D.1068, N.1070 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.376, A:N.1070 NAG.3: 4 residues within 4Å: Chain A: W.353, N.367, S.369 Ligands: NAG.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.369 NAG.4: 5 residues within 4Å: Chain A: R.360, N.363, S.366, N.367 Ligands: NAG.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.360

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

PEE.5: 9 residues within 4Å: Chain A: W.1048, D.1100, H.1101, G.1103, N.1104, R.1439, A.1440, I.1443, V.1447 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:W.1048, A:W.1048, A:A.1440, A:I.1443, A:V.1447 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.6: 9 residues within 4Å: Chain A: K.976, W.977, F.1014, S.1018, Q.1024, T.1027, V.1031, V.1367, Y.1368 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:W.977, A:F.1014, A:F.1014, A:T.1027, A:V.1367, A:Y.1368 Hydrogen bonds: A:T.1027 PEE.7: 15 residues within 4Å: Chain A: I.330, L.334, N.385, S.386, W.446, H.447, L.449, F.450, I.453, S.1315, T.1317, V.1321, L.1324, I.1327, G.1328 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:I.330, A:L.334, A:W.446, A:W.446, A:L.449, A:I.453, A:V.1321, A:I.1327 Hydrogen bonds: A:N.385, A:S.1315, A:S.1315, A:T.1317 Salt bridges: A:H.447 PEE.8: 10 residues within 4Å: Chain A: T.415, G.417, W.418, F.420, L.421, F.424, I.773, P.774, V.777, A.778 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.420, A:L.421, A:F.424, A:F.424, A:I.773, A:P.774 Hydrogen bonds: A:T.415 PEE.9: 11 residues within 4Å: Chain A: P.255, W.256, L.259, L.287, W.290, W.299, R.300, V.303, I.709, F.710, P.774 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.259, A:W.290, A:V.303, A:I.709, A:F.710, A:F.710, A:P.774 Hydrogen bonds: A:W.256, A:R.300

1 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.10: 10 residues within 4Å: Chain A: S.387, G.388, P.445, W.446, I.448, L.449, I.452, S.1358, F.1362, G.1395 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:P.445, A:W.446, A:W.446, A:I.448, A:L.449, A:I.452, A:F.1362

1 x X7L: N-[6-(cyclopentylmethoxy)-1,3-benzothiazol-2-yl]-4-{[(1S,2S)-2-(dimethylamino)cyclohexyl]amino}-2-fluorobenzene-1-sulfonamide(Non-covalent)

X7L.11: 17 residues within 4Å: Chain A: E.1255, Y.1258, W.1259, N.1261, V.1262, I.1298, S.1299, G.1302, M.1303, L.1305, D.1307, F.1319, I.1322, R.1323, A.1325, R.1326, R.1329 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:Y.1258, A:V.1262, A:I.1298, A:L.1305, A:D.1307, A:A.1325 Hydrogen bonds: A:R.1323, A:R.1329, A:R.1329 Water bridges: A:N.1261, A:R.1326 Salt bridges: A:E.1255 pi-Stacking: A:Y.1258

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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