SMTL ID : 5ek0.1

Human Nav1.7-VSD4-NavAb in complex with GX-936.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.53 Å

Oligo State

homo-tetramer

Ligands

21 x PX4: 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE(Non-covalent)

PX4.1: 9 residues within 4Å: Chain A: L.180, F.181, Y.220, P.221, Y.222, A.223, V.225 Chain D: T.122, R.125 Ligand excluded by PLIP PX4.2: 13 residues within 4Å: Chain A: M.166, F.170, T.191, G.193, E.194, F.196, Y.197, F.200 Chain B: M.217, P.221, W.224, I.228, F.232 Ligand excluded by PLIP PX4.3: 1 residues within 4Å: Chain A: L.168 Ligand excluded by PLIP PX4.4: 3 residues within 4Å: Chain A: M.44, Q.144, M.145 Ligand excluded by PLIP PX4.5: 1 residues within 4Å: Chain A: L.42 Ligand excluded by PLIP PX4.6: 5 residues within 4Å: Chain A: F.200, T.204, M.238 Chain B: F.232, T.235 Ligand excluded by PLIP PX4.7: 4 residues within 4Å: Chain A: Q.56, E.60, D.112 Ligands: 5P2.8 Ligand excluded by PLIP PX4.9: 8 residues within 4Å: Chain A: T.122, L.123, R.125 Chain B: F.181, Y.220, P.221, Y.222, A.223 Ligand excluded by PLIP PX4.10: 13 residues within 4Å: Chain B: M.166, F.170, T.191, L.192, G.193, E.194, F.196, Y.197, F.200 Chain C: M.217, P.221, W.224, F.232 Ligand excluded by PLIP PX4.11: 4 residues within 4Å: Chain B: Q.144, M.145 Chain C: P.157, L.160 Ligand excluded by PLIP PX4.12: 3 residues within 4Å: Chain B: M.203, T.204, M.238 Ligand excluded by PLIP PX4.13: 5 residues within 4Å: Chain B: Q.56, E.60, W.64, D.112 Ligands: 5P2.14 Ligand excluded by PLIP PX4.15: 6 residues within 4Å: Chain B: T.122 Chain C: F.181, Y.220, P.221, Y.222, A.223 Ligand excluded by PLIP PX4.16: 14 residues within 4Å: Chain C: I.163, T.167, Y.171, T.191, G.193, E.194, F.196, Y.197, F.200 Chain D: M.217, P.221, Y.222, W.224, I.228 Ligand excluded by PLIP PX4.17: 2 residues within 4Å: Chain C: Q.144 Chain D: L.168 Ligand excluded by PLIP PX4.18: 4 residues within 4Å: Chain C: E.60, W.64, D.112 Ligands: 5P2.19 Ligand excluded by PLIP PX4.20: 9 residues within 4Å: Chain A: M.217, W.224, F.232 Chain D: M.166, F.170, G.193, E.194, F.196, F.200 Ligand excluded by PLIP PX4.21: 9 residues within 4Å: Chain C: T.122, R.125, V.126 Chain D: L.180, F.181, Y.220, P.221, Y.222, A.223 Ligand excluded by PLIP PX4.22: 3 residues within 4Å: Chain A: T.235 Chain D: M.203, T.204 Ligand excluded by PLIP PX4.23: 3 residues within 4Å: Chain D: L.42, T.46, I.65 Ligand excluded by PLIP PX4.24: 2 residues within 4Å: Chain D: E.60 Ligands: 5P2.25 Ligand excluded by PLIP

4 x 5P2: 3-cyano-4-[2-[2-(1-ethylazetidin-3-yl)pyrazol-3-yl]-4-(trifluoromethyl)phenoxy]-~{N}-(1,2,4-thiadiazol-5-yl)benzenesulfonamide(Non-covalent)

5P2.8: 19 residues within 4Å: Chain A: E.60, Y.63, W.64, N.66, V.67, S.104, G.107, M.108, F.109, A.111, D.112, E.115, T.116, F.124, R.128, A.130, R.131, R.134 Ligands: PX4.7 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:Y.63, A:W.64, A:W.64, A:D.112, A:E.115 Hydrogen bonds: A:E.60, A:R.131, A:R.134, A:R.134 Salt bridges: A:D.112 pi-Stacking: A:Y.63, A:Y.63 5P2.14: 18 residues within 4Å: Chain B: E.60, Y.63, W.64, N.66, V.67, S.104, G.107, M.108, F.109, A.111, D.112, E.115, F.124, R.128, A.130, R.131, R.134 Ligands: PX4.13 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:Y.63, B:Y.63, B:W.64, B:F.109, B:D.112 Hydrogen bonds: B:R.128, B:R.134, B:R.134 Salt bridges: B:E.60, B:D.112 pi-Stacking: B:Y.63, B:W.64 5P2.19: 20 residues within 4Å: Chain C: E.60, Y.63, W.64, N.66, V.67, S.104, G.107, M.108, F.109, A.111, D.112, E.115, T.116, F.124, I.127, R.128, A.130, R.131, R.134 Ligands: PX4.18 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:Y.63, C:W.64, C:W.64, C:V.67, C:D.112 Hydrogen bonds: C:R.131, C:R.134, C:R.134 Salt bridges: C:E.60, C:D.112, C:E.115 pi-Stacking: C:Y.63 5P2.25: 19 residues within 4Å: Chain D: E.60, Y.63, W.64, N.66, V.67, I.70, S.104, G.107, M.108, F.109, A.111, D.112, E.115, F.124, R.128, A.130, R.131, R.134 Ligands: PX4.24 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:Y.63, D:W.64, D:V.67, D:D.112, D:E.115 Hydrogen bonds: D:R.128, D:R.134, D:R.134 Salt bridges: D:E.60, D:D.112 pi-Stacking: D:Y.63, D:W.64

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ahuja, S. et al., Structural basis of Nav1.7 inhibition by an isoform-selective small-molecule antagonist. Science (2015)

Release Date

2015-12-23

Peptides

Chimera of bacterial Ion transport protein and human Sodium channel protein type 9 subunit alpha: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Membrane

We predict this structure to be a membrane protein.
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Chimera of bacterial Ion transport protein and human Sodium channel protein type 9 subunit alpha