SMTL ID : 8i5y.1

Structure of human Nav1.7 in complex with vixotrigine

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-mer

Ligands

3 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 5 residues within 4Å: Chain A: N.1392, T.1394, D.1395, F.1399, S.1417 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 5 residues within 4Å: Chain A: P.1405, N.1406, S.1408, E.1409, K.1463 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 6 residues within 4Å: Chain B: F.54, E.56, R.72, Y.124, L.126, N.135 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Y.124 Hydrogen bonds: B:R.72

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

NAG.4: 1 residues within 4Å: Chain A: N.323 No protein-ligand interaction detected (PLIP) NAG.9: 1 residues within 4Å: Chain A: N.1415 No protein-ligand interaction detected (PLIP) NAG.32: 5 residues within 4Å: Chain B: V.91, W.92, N.93, R.96, F.107 No protein-ligand interaction detected (PLIP) NAG.33: 2 residues within 4Å: Chain B: G.33, N.110 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.33 NAG.34: 3 residues within 4Å: Chain B: R.89, T.112, N.114 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:T.112 Hydrogen bonds: B:N.114

1 x P5S: O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine(Non-covalent)

P5S.5: 12 residues within 4Å: Chain A: W.1218, W.1219, R.1222, Y.1226, L.1282, W.1285, I.1286, A.1287, G.1289, Y.1290, K.1291 Ligands: LPE.28 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:W.1218, A:L.1282, A:W.1285, A:I.1286, A:Y.1290, A:Y.1290 Salt bridges: A:R.1222, A:R.1222

4 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.6: 3 residues within 4Å: Chain A: T.1295, A.1297, W.1300 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:A.1297, A:W.1300, A:W.1300, A:W.1300 Y01.7: 11 residues within 4Å: Chain A: V.795, T.798, L.799, L.885, S.888, W.889, P.890, E.1021, L.1028, I.1370, L.1373 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:V.795, A:T.798, A:L.799, A:L.885, A:W.889, A:W.889, A:W.889, A:L.1028, A:I.1370, A:L.1373 Hydrogen bonds: A:E.1021 Y01.10: 2 residues within 4Å: Chain A: Y.1469, Y.1472 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.1472, A:Y.1472 Hydrogen bonds: A:Y.1469 Y01.31: 13 residues within 4Å: Chain A: A.802, H.805, P.807, L.1369, I.1370, L.1373, N.1431, V.1432, G.1433, Y.1436 Ligands: LPE.13, LPE.16, PCW.17 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:A.802, A:L.1369, A:I.1370, A:L.1373, A:N.1431, A:V.1432 Hydrogen bonds: A:N.1431 Salt bridges: A:H.805

1 x 9Z9: (3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en(Non-covalent)

9Z9.8: 12 residues within 4Å: Chain A: L.438, A.442, E.446, Q.450, F.1003, L.1004, L.1007, L.1008, I.1493, I.1497, I.1799, F.1803 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:L.438, A:A.442, A:F.1003, A:L.1004, A:L.1007, A:L.1008, A:I.1493, A:I.1493, A:I.1497, A:I.1799, A:F.1803

1 x TB4: Vixotrigine(Non-covalent)

TB4.11: 13 residues within 4Å: Chain A: Q.400, I.426, F.427, F.431, L.1691, F.1732, T.1735, T.1736, V.1791, Y.1795 Ligands: 1PW.15, LPE.22, LPE.24 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.427, A:F.431, A:L.1691, A:F.1732, A:T.1736, A:V.1791

1 x NA: SODIUM ION(Non-functional Binders)

NA.12: 6 residues within 4Å: Chain A: D.401, Y.402, E.967, W.968, I.969, E.970 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.401, A:W.968, A:I.969, A:E.970

14 x LPE: 1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE(Non-covalent)(Non-functional Binders)

LPE.13: 5 residues within 4Å: Chain A: M.803, H.805, F.812 Ligands: LPE.16, Y01.31 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:H.805 LPE.14: 9 residues within 4Å: Chain A: S.1750, P.1773, S.1774, I.1777, F.1778, V.1781, S.1782 Ligands: 1PW.15, PCW.17 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.1777, A:F.1778, A:F.1778, A:V.1781 Hydrogen bonds: A:S.1750 LPE.16: 3 residues within 4Å: Ligands: LPE.13, PCW.17, Y01.31 No protein-ligand interaction detected (PLIP) LPE.18: 9 residues within 4Å: Chain A: L.1335, I.1697, Y.1698, F.1701, N.1705, V.1775, F.1778, Y.1779 Ligands: LPE.19 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.1698 pi-Cation interactions: A:F.1701 LPE.19: 11 residues within 4Å: Chain A: A.1297, W.1298, L.1301, L.1332, L.1335, L.1338, L.1341, V.1351, N.1352, I.1355 Ligands: LPE.18 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.1332, A:L.1338 LPE.22: 8 residues within 4Å: Chain A: E.1517, Q.1518, Y.1521, L.1681, P.1682, L.1684, F.1685 Ligands: TB4.11 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.1681 Hydrogen bonds: A:Q.1518 Salt bridges: A:E.1517 pi-Cation interactions: A:Y.1521 LPE.23: 4 residues within 4Å: Chain A: Y.1521, A.1524, M.1525, L.1681 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.1681 LPE.24: 10 residues within 4Å: Chain A: T.359, D.360, K.416, T.417, V.423, M.1695, M.1728, F.1732 Ligands: TB4.11, LPE.25 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.423, A:F.1732 Hydrogen bonds: A:T.417 LPE.25: 7 residues within 4Å: Chain A: D.1253, Y.1255, R.1258, T.1723, G.1725 Ligands: LPE.24, LPE.26 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.1255 Salt bridges: A:K.416 LPE.26: 10 residues within 4Å: Chain A: S.1246, G.1247, A.1250, F.1251, K.1259, M.1347, L.1689, F.1696, F.1724 Ligands: LPE.25 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.1689, A:F.1696, A:F.1696 Hydrogen bonds: A:A.1250 LPE.27: 8 residues within 4Å: Chain A: V.293, F.294, S.297, F.387, F.391, M.1569, L.1663, A.1667 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.387, A:F.391, A:F.391 Hydrogen bonds: A:S.297 LPE.28: 2 residues within 4Å: Chain A: K.1291 Ligands: P5S.5 No protein-ligand interaction detected (PLIP) LPE.35: 8 residues within 4Å: Chain A: K.1227, I.1228, H.1231, F.1234, F.1237 Chain B: W.173, E.177, C.181 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Salt bridges: B:E.177 Hydrogen bonds: A:F.1234 pi-Cation interactions: A:H.1231 LPE.36: 3 residues within 4Å: Chain B: M.178, I.179, Y.182 No protein-ligand interaction detected (PLIP)

1 x 1PW: (2S,3R,4E)-2-(acetylamino)-3-hydroxyoctadec-4-en-1-yl dihydrogen phosphate(Non-covalent)

1PW.15: 15 residues within 4Å: Chain A: I.1361, M.1362, L.1365, T.1444, T.1735, T.1736, S.1737, I.1784, I.1785, S.1787, F.1788, L.1789 Ligands: TB4.11, LPE.14, PCW.17 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:I.1361, A:T.1444, A:I.1785, A:F.1788, A:L.1789 Hydrogen bonds: A:S.1737, A:S.1737

5 x PCW: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE(Non-covalent)

PCW.17: 16 residues within 4Å: Chain A: L.1365, C.1368, L.1369, W.1372, N.1431, G.1433, L.1434, L.1437, L.1440, I.1777, V.1781, I.1785 Ligands: LPE.14, 1PW.15, LPE.16, Y01.31 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:L.1365, A:L.1369, A:W.1372, A:W.1372, A:L.1434, A:L.1437, A:L.1440, A:I.1777, A:V.1781, A:I.1785 Hydrogen bonds: A:N.1431 PCW.20: 15 residues within 4Å: Chain A: Y.379, G.380, Y.381, S.388, W.389, F.391, F.395, Q.981, A.982, L.985, I.986, M.989, M.990, V.993, I.994 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:W.389, A:F.391, A:F.391, A:F.395, A:F.395, A:L.985, A:I.986, A:M.989, A:V.993, A:I.994 Hydrogen bonds: A:S.388, A:Q.981 PCW.21: 11 residues within 4Å: Chain A: L.1528, K.1531, T.1615, V.1616, G.1617, I.1620, F.1621, V.1624, L.1654, I.1657 Ligands: PCW.29 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.1620, A:F.1621, A:F.1621, A:I.1657 Hydrogen bonds: A:G.1617 Salt bridges: A:K.1531 PCW.29: 18 residues within 4Å: Chain A: F.294, C.295, V.298, L.1528, G.1529, K.1531, G.1617, W.1618, F.1621, L.1661, V.1664, K.1668, R.1671, T.1672, L.1674, F.1675, M.1678 Ligands: PCW.21 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:F.294, A:V.298, A:W.1618, A:W.1618, A:F.1621, A:F.1621, A:L.1661, A:V.1664, A:L.1674, A:L.1674 Hydrogen bonds: A:T.1672 Salt bridges: A:K.1668, A:R.1671 PCW.30: 7 residues within 4Å: Chain A: H.1611, F.1614, F.1623, V.1624, I.1627, I.1628, V.1631 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.1623, A:I.1627, A:I.1628, A:V.1631

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wu, Q. et al., Structural mapping of Na v 1.7 antagonists. Nat Commun (2023)

Release Date

2023-06-14

Peptides

Sodium channel protein type 9 subunit alpha: A
Sodium channel subunit beta-1: B
Sodium channel subunit beta-2: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Membrane

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

Sodium channel subunit beta-1

Sodium channel subunit beta-2

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