SMTL ID : 8ycp.1

structure of human trpv1 in complex with BC5

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

4 x 01: (1~{R},2~{S})-1-butyl-~{N}-(2,6-dimethylphenyl)-1-[5-[(2~{S})-2-[(2,6-dimethylphenyl)carbamoyl]piperidin-1-yl]pentyl]piperidin-1-ium-2-carboxamide

01.1: 17 residues within 4Å: Chain A: R.301, D.400, S.401, Y.402, S.403, L.406, T.441, L.444, R.448, I.460, E.461, K.462, I.464, Q.592, I.595 Chain C: F.478, L.561 15 PLIP interactions: 13 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:Y.402, A:L.406, A:L.406, A:L.444, A:I.460, A:E.461, A:I.464, A:Q.592, A:I.595, C:F.478, C:L.561 Hydrogen bonds: A:Y.402, A:E.461, A:Q.592 Salt bridges: A:E.461 01.4: 16 residues within 4Å: Chain B: R.301, D.400, Y.402, S.403, L.406, L.438, T.441, L.444, R.448, E.461, I.464, L.591, Q.592, I.595 Chain D: F.478, L.561 14 PLIP interactions: 2 interactions with chain D, 12 interactions with chain B Hydrophobic interactions: D:F.478, D:L.561, B:Y.402, B:L.406, B:T.441, B:L.444, B:E.461, B:I.464, B:L.591, B:Q.592, B:I.595 Hydrogen bonds: B:D.400, B:Q.592 Salt bridges: B:E.461 01.7: 18 residues within 4Å: Chain B: F.478, F.482, L.561 Chain C: R.301, V.399, D.400, S.401, Y.402, S.403, L.406, L.438, T.441, L.444, R.448, I.460, E.461, I.464, Q.592 16 PLIP interactions: 13 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:Y.402, C:Y.402, C:L.406, C:L.438, C:T.441, C:L.444, C:I.460, C:E.461, C:I.464, C:Q.592, B:F.478, B:L.561, B:L.561 Hydrogen bonds: C:S.401, C:Q.592 Salt bridges: C:E.461 01.8: 16 residues within 4Å: Chain A: F.478, F.482, L.561 Chain D: R.301, D.400, Y.402, S.403, L.406, L.438, T.441, L.444, R.448, A.457, E.461, I.464, Q.592 17 PLIP interactions: 14 interactions with chain D, 3 interactions with chain A Hydrophobic interactions: D:Y.402, D:L.406, D:L.438, D:T.441, D:L.444, D:E.461, D:E.461, D:I.464, A:F.478, A:F.482, A:L.561 Hydrogen bonds: D:Y.402, D:S.403, D:R.448, D:E.461, D:Q.592 Salt bridges: D:E.461

4 x 6OU: [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate(Non-covalent)

6OU.2: 7 residues within 4Å: Chain A: M.472, I.476, L.479, S.521, Y.523, C.526 Chain C: L.556 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.476, A:L.479, A:Y.523 Hydrogen bonds: A:S.521 6OU.5: 9 residues within 4Å: Chain B: M.472, I.476, S.521, L.522, Y.523, F.530 Chain D: K.548, A.549, L.556 10 PLIP interactions: 7 interactions with chain B, 3 interactions with chain D Hydrophobic interactions: B:I.476, B:L.522, B:Y.523, B:Y.523, B:F.530, D:K.548, D:A.549, D:L.556 Hydrogen bonds: B:S.521, B:S.521 6OU.6: 11 residues within 4Å: Chain B: K.548, I.553, L.556, A.557, L.561 Chain C: M.472, I.476, L.479, Y.523, L.527, F.530 13 PLIP interactions: 5 interactions with chain B, 8 interactions with chain C Hydrophobic interactions: B:I.553, B:L.556, B:A.557, B:L.561, C:I.476, C:L.479, C:Y.523, C:Y.523, C:Y.523, C:L.527, C:F.530, C:F.530 Salt bridges: B:K.548 6OU.9: 12 residues within 4Å: Chain A: K.548, A.549, I.552, L.556 Chain B: Y.345 Chain D: M.472, I.476, L.479, S.521, Y.523, C.526, F.530 9 PLIP interactions: 6 interactions with chain D, 3 interactions with chain A Hydrophobic interactions: D:I.476, D:L.479, D:Y.523, D:F.530, D:F.530, A:K.548, A:A.549, A:L.556 Hydrogen bonds: D:S.521

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

NA.3: 4 residues within 4Å: Chain A: G.535 Chain B: G.535 Chain C: G.535 Chain D: G.535 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.535

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hu, S.L. et al., Sequential multitarget modulation: Developing Ultra-long-acting sensory-specific local anesthetics for postoperative pain. To Be Published

Release Date

2025-01-29

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