SMTL ID : 8jqr.1

Structure of human TRPV1 in complex with antagonist

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

4 x EZI: 4-(7-Hydroxy-2-isopropyl-4-oxoquinazolin-3(4H)-yl)benzonitrile(Non-covalent)

EZI.1: 15 residues within 4Å: Chain A: Y.511, S.512, L.515, T.550, N.551, L.553, Y.554, T.556, R.557, G.563, A.566, V.567, W.698, Q.701 Ligands: CLR.2 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.515, A:L.553, A:A.566, A:A.566 Hydrogen bonds: A:R.557 pi-Stacking: A:Y.511 pi-Cation interactions: A:R.557 EZI.3: 15 residues within 4Å: Chain B: Y.511, S.512, L.515, T.550, N.551, L.553, Y.554, T.556, R.557, G.563, A.566, V.567, W.698, Q.701 Ligands: CLR.4 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:L.515, B:L.553, B:A.566, B:A.566 Hydrogen bonds: B:R.557 pi-Stacking: B:Y.511 pi-Cation interactions: B:R.557 EZI.5: 16 residues within 4Å: Chain C: Y.511, S.512, L.515, L.547, T.550, N.551, L.553, Y.554, T.556, R.557, G.563, A.566, V.567, W.698, Q.701 Ligands: CLR.6 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:L.515, C:L.553, C:A.566, C:A.566 Hydrogen bonds: C:R.557 pi-Cation interactions: C:R.557 EZI.7: 16 residues within 4Å: Chain D: Y.511, S.512, L.515, L.547, T.550, N.551, L.553, Y.554, T.556, R.557, G.563, A.566, V.567, W.698, Q.701 Ligands: CLR.8 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:L.515, D:L.553, D:A.566, D:A.566 Hydrogen bonds: D:R.557 pi-Stacking: D:Y.511 pi-Cation interactions: D:R.557

4 x CLR: CHOLESTEROL(Non-covalent)

CLR.2: 12 residues within 4Å: Chain A: F.507, V.508, Y.511, A.546, L.547, T.550, E.570, I.573, L.574 Chain B: F.591, L.670 Ligands: EZI.1 7 PLIP interactions: 2 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:F.591, B:L.670, A:Y.511, A:Y.511, A:I.573, A:I.573 Hydrogen bonds: A:V.508 CLR.4: 13 residues within 4Å: Chain B: F.507, V.508, Y.511, F.543, L.547, T.550, E.570, I.573, L.574 Chain D: F.591, A.666, L.670 Ligands: EZI.3 9 PLIP interactions: 3 interactions with chain D, 6 interactions with chain B Hydrophobic interactions: D:F.591, D:A.666, D:L.670, B:Y.511, B:Y.511, B:L.547, B:I.573, B:I.573 Hydrogen bonds: B:V.508 CLR.6: 13 residues within 4Å: Chain A: F.591, L.670 Chain C: F.507, V.508, Y.511, L.515, A.546, L.547, T.550, E.570, I.573, L.574 Ligands: EZI.5 9 PLIP interactions: 2 interactions with chain A, 7 interactions with chain C Hydrophobic interactions: A:F.591, A:L.670, C:Y.511, C:Y.511, C:L.515, C:I.573, C:I.573, C:L.574 Hydrogen bonds: C:V.508 CLR.8: 13 residues within 4Å: Chain C: F.591, L.670 Chain D: F.507, V.508, Y.511, L.515, A.546, L.547, T.550, E.570, I.573, L.574 Ligands: EZI.7 10 PLIP interactions: 2 interactions with chain C, 8 interactions with chain D Hydrophobic interactions: C:F.591, C:L.670, D:Y.511, D:Y.511, D:L.515, D:L.547, D:I.573, D:I.573, D:L.574 Hydrogen bonds: D:V.508

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fan, J. et al., Structural basis of TRPV1 inhibition by SAF312 and cholesterol. Nat Commun (2024)

Release Date

2024-08-14

Peptides

Transient receptor potential cation channel subfamily V member 1,PreScission Site,Green fluorescent protein: 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,PreScission Site,Green fluorescent protein

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