SMTL ID : 8f0q.1

Structure of VSD4-NaV1.7-NaVPas channel chimera bound to the acylsulfonamide inhibitor GDC-0310

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

monomer

Ligands

1 x NAG- NAG- BMA- BMA: beta-D-mannopyranose-(1-3)-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.1: 8 residues within 4Å: Chain A: F.356, W.361, N.385, T.397, C.398, L.399, Q.400 Ligands: BMA.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.361

1 x BMA: beta-D-mannopyranose(Non-functional Binders)

BMA.2: 1 residues within 4Å: Ligands: NAG-NAG-BMA-BMA.1 No protein-ligand interaction detected (PLIP)

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

NAG.3: 4 residues within 4Å: Chain A: W.353, N.367, S.369 Ligands: NAG.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.367, A:S.369 NAG.4: 2 residues within 4Å: Chain A: N.363 Ligands: NAG.3 No protein-ligand interaction detected (PLIP)

1 x X7R: 5-cyclopropyl-4-({1-[(1S)-1-(3,5-dichlorophenyl)ethyl]piperidin-4-yl}methoxy)-2-fluoro-N-(methanesulfonyl)benzamide(Non-covalent)

X7R.5: 16 residues within 4Å: Chain A: Y.1258, N.1261, I.1265, I.1298, S.1299, V.1301, G.1302, L.1305, A.1306, I.1309, F.1319, I.1322, R.1323, A.1325, R.1326, R.1329 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.1305, A:A.1306, A:I.1309, A:F.1319, A:I.1322 Hydrogen bonds: A:R.1323, A:R.1326, A:R.1329, A:R.1329

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

PEE.6: 8 residues within 4Å: Chain A: I.1041, W.1048, D.1100, H.1101, G.1103, N.1104, R.1439, A.1440 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:W.1048, A:A.1440 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.7: 12 residues within 4Å: Chain A: K.976, W.977, F.1011, F.1014, S.1018, Q.1024, T.1027, L.1030, V.1031, I.1037, V.1367, Y.1368 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:W.977, A:F.1011, A:F.1014, A:F.1014, A:T.1027, A:L.1030, A:L.1030, A:I.1037, A:V.1367, A:Y.1368, A:Y.1368 Hydrogen bonds: A:S.1018, A:Q.1024 Salt bridges: A:K.976 PEE.8: 13 residues within 4Å: Chain A: I.330, N.385, S.386, W.446, H.447, L.449, F.450, S.1315, T.1317, V.1321, L.1324, G.1328, L.1331 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:I.330, A:W.446, A:W.446, A:L.449, A:L.1324, A:L.1331 Hydrogen bonds: A:N.385, A:S.1315, A:S.1315, A:T.1317, A:T.1317 Salt bridges: A:H.447 PEE.9: 9 residues within 4Å: Chain A: T.415, G.417, W.418, F.420, L.421, F.424, V.777, A.778, F.781 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.420, A:F.424, A:F.424, A:F.781 Hydrogen bonds: A:T.415 PEE.10: 8 residues within 4Å: Chain A: P.255, W.256, L.287, W.290, V.303, D.304, I.709, F.710 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.287, A:W.290, A:I.709, A:F.710, A:F.710 Hydrogen bonds: A:W.256, A:D.304

1 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.11: 7 residues within 4Å: Chain A: S.387, G.388, P.445, W.446, F.1362, G.1395, I.1398 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:P.445, A:W.446, A:W.446, 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

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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