SMTL ID : 8gfa.1

Cryo-EM structure of human TRPV1 in complex with the analgesic drug SB-366791

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

36 x POV: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate(Non-covalent)

POV.1: 26 residues within 4Å: Chain A: I.575, L.579, M.583, Y.586, I.587, L.590, S.632, L.633, Y.634, S.635, C.637, L.638, F.641 Chain B: K.659, A.660, I.663, I.664, L.667, A.668, I.671, L.672 Ligands: ZEI.2, POV.4, POV.13, POV.42, POV.45 Ligand excluded by PLIP POV.3: 20 residues within 4Å: Chain A: F.439, N.440, V.443, Y.444, L.446, Y.447, I.450, T.478, I.481, L.482, L.485, G.486, Y.489, F.490, R.493, E.515, F.518, Y.556, Y.557 Ligands: POV.7 Ligand excluded by PLIP POV.4: 17 residues within 4Å: Chain A: K.506, F.509, V.510, L.576, R.577, C.580, R.581, M.583, F.584, I.587 Chain D: Q.563, M.564 Ligands: POV.1, POV.13, POV.42, POV.44, POV.45 Ligand excluded by PLIP POV.5: 16 residues within 4Å: Chain A: F.451, A.454, A.455, M.468, V.477, E.480, I.481, S.483, V.484, M.525, T.528, V.529, Y.532, F.533, Y.539, M.543 Ligand excluded by PLIP POV.6: 21 residues within 4Å: Chain A: I.449, T.452, M.453, Y.456, Y.457, W.551 Chain B: F.584, I.587, V.588, L.590, F.591, T.595, N.631, S.632, L.633, C.637 Ligands: POV.7, POV.8, POV.9, POV.15, POV.18 Ligand excluded by PLIP POV.7: 19 residues within 4Å: Chain A: L.446, I.449, I.450, M.453, A.454, Y.456, Y.457, R.458, K.470, T.471, G.472, F.475, R.476, T.478, G.479, L.482 Ligands: POV.3, POV.6, POV.9 Ligand excluded by PLIP POV.8: 21 residues within 4Å: Chain A: W.429, K.434, Y.438, F.441, L.442, C.445, I.449, W.551, M.554, L.555, Y.557, T.558, G.560, F.561, Q.562, Q.563, M.564 Chain B: F.584, V.588 Ligands: POV.6, POV.18 Ligand excluded by PLIP POV.9: 9 residues within 4Å: Chain A: I.449, M.453, Y.457 Chain B: I.587 Ligands: POV.6, POV.7, POV.14, POV.15, POV.18 Ligand excluded by PLIP POV.11: 20 residues within 4Å: Chain A: D.657, F.658, K.659, A.660, V.661, I.664 Chain D: Y.513, M.516, L.517, L.520, F.524, A.541, F.545, L.549, I.575 Ligands: POV.33, POV.37, ZEI.38, POV.40, DU0.46 Ligand excluded by PLIP POV.13: 20 residues within 4Å: Chain A: Y.513, M.516, L.517, L.520, F.524, A.541, F.545, L.549, I.575 Chain B: D.657, F.658, K.659, A.660, V.661, I.664 Ligands: POV.1, ZEI.2, POV.4, DU0.10, POV.45 Ligand excluded by PLIP POV.14: 20 residues within 4Å: Chain B: Y.513, M.516, L.517, L.520, F.524, A.541, F.545, L.549, I.575 Chain C: D.657, F.658, K.659, A.660, V.661, I.664 Ligands: POV.9, POV.15, ZEI.16, POV.18, DU0.24 Ligand excluded by PLIP POV.15: 26 residues within 4Å: Chain B: I.575, L.579, M.583, Y.586, I.587, L.590, S.632, L.633, Y.634, S.635, C.637, L.638, F.641 Chain C: K.659, A.660, I.663, I.664, L.667, A.668, I.671, L.672 Ligands: POV.6, POV.9, POV.14, ZEI.16, POV.18 Ligand excluded by PLIP POV.17: 20 residues within 4Å: Chain B: F.439, N.440, V.443, Y.444, L.446, Y.447, I.450, T.478, I.481, L.482, L.485, G.486, Y.489, F.490, R.493, E.515, F.518, Y.556, Y.557 Ligands: POV.21 Ligand excluded by PLIP POV.18: 17 residues within 4Å: Chain A: Q.563, M.564 Chain B: K.506, F.509, V.510, L.576, R.577, C.580, R.581, M.583, F.584, I.587 Ligands: POV.6, POV.8, POV.9, POV.14, POV.15 Ligand excluded by PLIP POV.19: 16 residues within 4Å: Chain B: F.451, A.454, A.455, M.468, V.477, E.480, I.481, S.483, V.484, M.525, T.528, V.529, Y.532, F.533, Y.539, M.543 Ligand excluded by PLIP POV.20: 21 residues within 4Å: Chain B: I.449, T.452, M.453, Y.456, Y.457, W.551 Chain C: F.584, I.587, V.588, L.590, F.591, T.595, N.631, S.632, L.633, C.637 Ligands: POV.21, POV.22, POV.23, POV.25, POV.28 Ligand excluded by PLIP POV.21: 19 residues within 4Å: Chain B: L.446, I.449, I.450, M.453, A.454, Y.456, Y.457, R.458, K.470, T.471, G.472, F.475, R.476, T.478, G.479, L.482 Ligands: POV.17, POV.20, POV.23 Ligand excluded by PLIP POV.22: 21 residues within 4Å: Chain B: W.429, K.434, Y.438, F.441, L.442, C.445, I.449, W.551, M.554, L.555, Y.557, T.558, G.560, F.561, Q.562, Q.563, M.564 Chain C: F.584, V.588 Ligands: POV.20, POV.28 Ligand excluded by PLIP POV.23: 9 residues within 4Å: Chain B: I.449, M.453, Y.457 Chain C: I.587 Ligands: POV.20, POV.21, POV.25, POV.28, POV.36 Ligand excluded by PLIP POV.25: 26 residues within 4Å: Chain C: I.575, L.579, M.583, Y.586, I.587, L.590, S.632, L.633, Y.634, S.635, C.637, L.638, F.641 Chain D: K.659, A.660, I.663, I.664, L.667, A.668, I.671, L.672 Ligands: POV.20, POV.23, ZEI.26, POV.28, POV.36 Ligand excluded by PLIP POV.27: 20 residues within 4Å: Chain C: F.439, N.440, V.443, Y.444, L.446, Y.447, I.450, T.478, I.481, L.482, L.485, G.486, Y.489, F.490, R.493, E.515, F.518, Y.556, Y.557 Ligands: POV.31 Ligand excluded by PLIP POV.28: 17 residues within 4Å: Chain B: Q.563, M.564 Chain C: K.506, F.509, V.510, L.576, R.577, C.580, R.581, M.583, F.584, I.587 Ligands: POV.20, POV.22, POV.23, POV.25, POV.36 Ligand excluded by PLIP POV.29: 16 residues within 4Å: Chain C: F.451, A.454, A.455, M.468, V.477, E.480, I.481, S.483, V.484, M.525, T.528, V.529, Y.532, F.533, Y.539, M.543 Ligand excluded by PLIP POV.30: 21 residues within 4Å: Chain C: I.449, T.452, M.453, Y.456, Y.457, W.551 Chain D: F.584, I.587, V.588, L.590, F.591, T.595, N.631, S.632, L.633, C.637 Ligands: POV.31, POV.32, POV.33, POV.37, POV.40 Ligand excluded by PLIP POV.31: 19 residues within 4Å: Chain C: L.446, I.449, I.450, M.453, A.454, Y.456, Y.457, R.458, K.470, T.471, G.472, F.475, R.476, T.478, G.479, L.482 Ligands: POV.27, POV.30, POV.33 Ligand excluded by PLIP POV.32: 21 residues within 4Å: Chain C: W.429, K.434, Y.438, F.441, L.442, C.445, I.449, W.551, M.554, L.555, Y.557, T.558, G.560, F.561, Q.562, Q.563, M.564 Chain D: F.584, V.588 Ligands: POV.30, POV.40 Ligand excluded by PLIP POV.33: 9 residues within 4Å: Chain C: I.449, M.453, Y.457 Chain D: I.587 Ligands: POV.11, POV.30, POV.31, POV.37, POV.40 Ligand excluded by PLIP POV.36: 20 residues within 4Å: Chain C: Y.513, M.516, L.517, L.520, F.524, A.541, F.545, L.549, I.575 Chain D: D.657, F.658, K.659, A.660, V.661, I.664 Ligands: POV.23, POV.25, ZEI.26, POV.28, DU0.34 Ligand excluded by PLIP POV.37: 26 residues within 4Å: Chain A: K.659, A.660, I.663, I.664, L.667, A.668, I.671, L.672 Chain D: I.575, L.579, M.583, Y.586, I.587, L.590, S.632, L.633, Y.634, S.635, C.637, L.638, F.641 Ligands: POV.11, POV.30, POV.33, ZEI.38, POV.40 Ligand excluded by PLIP POV.39: 20 residues within 4Å: Chain D: F.439, N.440, V.443, Y.444, L.446, Y.447, I.450, T.478, I.481, L.482, L.485, G.486, Y.489, F.490, R.493, E.515, F.518, Y.556, Y.557 Ligands: POV.43 Ligand excluded by PLIP POV.40: 17 residues within 4Å: Chain C: Q.563, M.564 Chain D: K.506, F.509, V.510, L.576, R.577, C.580, R.581, M.583, F.584, I.587 Ligands: POV.11, POV.30, POV.32, POV.33, POV.37 Ligand excluded by PLIP POV.41: 16 residues within 4Å: Chain D: F.451, A.454, A.455, M.468, V.477, E.480, I.481, S.483, V.484, M.525, T.528, V.529, Y.532, F.533, Y.539, M.543 Ligand excluded by PLIP POV.42: 21 residues within 4Å: Chain A: F.584, I.587, V.588, L.590, F.591, T.595, N.631, S.632, L.633, C.637 Chain D: I.449, T.452, M.453, Y.456, Y.457, W.551 Ligands: POV.1, POV.4, POV.43, POV.44, POV.45 Ligand excluded by PLIP POV.43: 19 residues within 4Å: Chain D: L.446, I.449, I.450, M.453, A.454, Y.456, Y.457, R.458, K.470, T.471, G.472, F.475, R.476, T.478, G.479, L.482 Ligands: POV.39, POV.42, POV.45 Ligand excluded by PLIP POV.44: 21 residues within 4Å: Chain A: F.584, V.588 Chain D: W.429, K.434, Y.438, F.441, L.442, C.445, I.449, W.551, M.554, L.555, Y.557, T.558, G.560, F.561, Q.562, Q.563, M.564 Ligands: POV.4, POV.42 Ligand excluded by PLIP POV.45: 9 residues within 4Å: Chain A: I.587 Chain D: I.449, M.453, Y.457 Ligands: POV.1, POV.4, POV.13, POV.42, POV.43 Ligand excluded by PLIP

4 x ZEI: (2E)-3-(4-chlorophenyl)-N-(3-methoxyphenyl)prop-2-enamide(Non-covalent)

ZEI.2: 21 residues within 4Å: Chain A: Y.513, S.514, L.517, F.545, A.548, L.549, T.552, N.553, L.555, Y.556, R.559, A.568, I.571, E.572, I.575 Chain B: F.593, L.665, A.668, L.672 Ligands: POV.1, POV.13 10 PLIP interactions: 3 interactions with chain B, 7 interactions with chain A Hydrophobic interactions: B:F.593, B:A.668, B:L.672, A:L.517, A:L.549, A:I.571, A:E.572 Hydrogen bonds: A:Y.513 Water bridges: A:Y.556 pi-Stacking: A:Y.513 ZEI.16: 21 residues within 4Å: Chain B: Y.513, S.514, L.517, F.545, A.548, L.549, T.552, N.553, L.555, Y.556, R.559, A.568, I.571, E.572, I.575 Chain C: F.593, L.665, A.668, L.672 Ligands: POV.14, POV.15 11 PLIP interactions: 8 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: B:L.517, B:L.549, B:I.571, B:E.572, B:I.575, C:F.593, C:A.668, C:L.672 Hydrogen bonds: B:Y.513 Water bridges: B:Y.556 pi-Stacking: B:Y.513 ZEI.26: 21 residues within 4Å: Chain C: Y.513, S.514, L.517, F.545, A.548, L.549, T.552, N.553, L.555, Y.556, R.559, A.568, I.571, E.572, I.575 Chain D: F.593, L.665, A.668, L.672 Ligands: POV.25, POV.36 10 PLIP interactions: 7 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:L.549, C:I.571, C:E.572, C:I.575, D:F.593, D:A.668, D:L.672 Hydrogen bonds: C:Y.513 Water bridges: C:Y.556 pi-Stacking: C:Y.513 ZEI.38: 21 residues within 4Å: Chain A: F.593, L.665, A.668, L.672 Chain D: Y.513, S.514, L.517, F.545, A.548, L.549, T.552, N.553, L.555, Y.556, R.559, A.568, I.571, E.572, I.575 Ligands: POV.11, POV.37 10 PLIP interactions: 7 interactions with chain D, 3 interactions with chain A Hydrophobic interactions: D:L.549, D:I.571, D:E.572, D:I.575, A:F.593, A:A.668, A:L.672 Hydrogen bonds: D:Y.513 Water bridges: D:Y.556 pi-Stacking: D:Y.513

4 x DU0: 2-[2-[(1~{S},2~{S},4~{S},5'~{R},6~{R},7~{S},8~{R},9~{S},12~{S},13~{R},16~{S})-5',7,9,13-tetramethylspiro[5-oxapentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icos-18-ene-6,2'-oxane]-16-yl]oxyethyl]propane-1,3-diol(Non-covalent)

DU0.10: 11 residues within 4Å: Chain A: L.520, L.523, F.524, A.527, L.531, L.536, E.538, A.541, S.542, F.545 Ligands: POV.13 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.523, A:L.536 DU0.24: 11 residues within 4Å: Chain B: L.520, L.523, F.524, A.527, L.531, L.536, E.538, A.541, S.542, F.545 Ligands: POV.14 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.523, B:L.536 DU0.34: 11 residues within 4Å: Chain C: L.520, L.523, F.524, A.527, L.531, L.536, E.538, A.541, S.542, F.545 Ligands: POV.36 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:L.523, C:L.536 DU0.46: 11 residues within 4Å: Chain D: L.520, L.523, F.524, A.527, L.531, L.536, E.538, A.541, S.542, F.545 Ligands: POV.11 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:L.523, D:L.536

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

NA.12: 5 residues within 4Å: Chain A: G.646 Chain B: G.646 Chain C: G.646 Chain D: G.646 Ligands: NA.35 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:G.646 NA.35: 5 residues within 4Å: Chain A: G.646 Chain B: G.646 Chain C: G.646 Chain D: G.646 Ligands: NA.12 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Neuberger, A. et al., Human TRPV1 structure and inhibition by the analgesic SB-366791. Nat Commun (2023)

Release Date

2023-05-10

Peptides

Transient receptor potential cation channel subfamily V member 1: 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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Transient receptor potential cation channel subfamily V member 1

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