SMTL ID : 7d4p.1

Structure of human TRPC5 in complex with clemizole

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

4 x GX0: 1-[(4-chlorophenyl)methyl]-2-(pyrrolidin-1-ylmethyl)benzimidazole(Non-covalent)

GX0.1: 12 residues within 4Å: Chain A: Y.374, F.414, G.417, E.418, D.439, M.442, N.443, Y.446, R.492, S.495, L.496, P.659 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:Y.374, A:Y.374, A:F.414, A:D.439, A:L.496, A:L.496, A:P.659 pi-Stacking: A:F.414 GX0.8: 12 residues within 4Å: Chain B: Y.374, F.414, G.417, E.418, D.439, M.442, N.443, Y.446, R.492, S.495, L.496, P.659 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:Y.374, B:Y.374, B:F.414, B:D.439, B:L.496, B:L.496, B:P.659 pi-Stacking: B:F.414 GX0.15: 12 residues within 4Å: Chain C: Y.374, F.414, G.417, E.418, D.439, M.442, N.443, Y.446, R.492, S.495, L.496, P.659 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:Y.374, C:Y.374, C:F.414, C:D.439, C:L.496, C:L.496, C:P.659 pi-Stacking: C:F.414 GX0.22: 12 residues within 4Å: Chain D: Y.374, F.414, G.417, E.418, D.439, M.442, N.443, Y.446, R.492, S.495, L.496, P.659 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:Y.374, D:Y.374, D:F.414, D:D.439, D:L.496, D:L.496, D:P.659 pi-Stacking: D:F.414

4 x PTY: PHOSPHATIDYLETHANOLAMINE(Non-covalent)

PTY.2: 13 residues within 4Å: Chain A: W.434, W.435, M.438, I.484, I.487, L.488, L.491, Q.507, L.514 Chain D: T.603, T.607 Ligands: POV.3, YZY.7 9 PLIP interactions: 7 interactions with chain A, 2 interactions with chain D Hydrophobic interactions: A:I.484, A:I.487, A:L.488, A:L.491, A:L.514, D:T.603, D:T.607 Hydrogen bonds: A:W.434, A:Q.507 PTY.9: 13 residues within 4Å: Chain A: T.603, T.607 Chain B: W.434, W.435, M.438, I.484, I.487, L.488, L.491, Q.507, L.514 Ligands: POV.10, YZY.14 9 PLIP interactions: 7 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:I.484, B:I.487, B:L.488, B:L.491, B:L.514, A:T.603, A:T.607 Hydrogen bonds: B:W.434, B:Q.507 PTY.16: 13 residues within 4Å: Chain B: T.603, T.607 Chain C: W.434, W.435, M.438, I.484, I.487, L.488, L.491, Q.507, L.514 Ligands: POV.17, YZY.21 9 PLIP interactions: 2 interactions with chain B, 7 interactions with chain C Hydrophobic interactions: B:T.603, B:T.607, C:I.484, C:I.487, C:L.488, C:L.491, C:L.514 Hydrogen bonds: C:W.434, C:Q.507 PTY.23: 13 residues within 4Å: Chain C: T.603, T.607 Chain D: W.434, W.435, M.438, I.484, I.487, L.488, L.491, Q.507, L.514 Ligands: POV.24, YZY.28 9 PLIP interactions: 7 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:I.484, D:I.487, D:L.488, D:L.491, D:L.514, C:T.603, C:T.607 Hydrogen bonds: D:W.434, D:Q.507

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

POV.3: 9 residues within 4Å: Chain A: S.444, L.445, A.448, W.472, I.477, L.481, I.484 Chain D: F.596 Ligands: PTY.2 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.445, A:A.448, A:L.481, A:I.484, A:I.484 Hydrogen bonds: A:W.472 POV.10: 9 residues within 4Å: Chain A: F.596 Chain B: S.444, L.445, A.448, W.472, I.477, L.481, I.484 Ligands: PTY.9 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:L.445, B:A.448, B:L.481, B:I.484, B:I.484 Hydrogen bonds: B:W.472 POV.17: 9 residues within 4Å: Chain B: F.596 Chain C: S.444, L.445, A.448, W.472, I.477, L.481, I.484 Ligands: PTY.16 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:L.445, C:A.448, C:L.481, C:I.484, C:I.484 Hydrogen bonds: C:W.472 POV.24: 9 residues within 4Å: Chain C: F.596 Chain D: S.444, L.445, A.448, W.472, I.477, L.481, I.484 Ligands: PTY.23 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:L.445, D:A.448, D:L.481, D:I.484, D:I.484 Hydrogen bonds: D:W.472

4 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.4: 13 residues within 4Å: Chain A: W.315, Y.316, F.364, F.367, T.371, L.375, L.496, F.497, A.499, N.500 Chain D: F.522, C.525, L.526 11 PLIP interactions: 7 interactions with chain A, 4 interactions with chain D Hydrophobic interactions: A:F.367, A:T.371, A:L.375, A:F.497, A:F.497, A:A.499, D:F.522, D:F.522, D:F.522, D:L.526 Hydrogen bonds: A:N.500 Y01.11: 13 residues within 4Å: Chain A: F.522, C.525, L.526 Chain B: W.315, Y.316, F.364, F.367, T.371, L.375, L.496, F.497, A.499, N.500 11 PLIP interactions: 7 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:F.367, B:T.371, B:L.375, B:F.497, B:F.497, B:A.499, A:F.522, A:F.522, A:F.522, A:L.526 Hydrogen bonds: B:N.500 Y01.18: 13 residues within 4Å: Chain B: F.522, C.525, L.526 Chain C: W.315, Y.316, F.364, F.367, T.371, L.375, L.496, F.497, A.499, N.500 11 PLIP interactions: 7 interactions with chain C, 4 interactions with chain B Hydrophobic interactions: C:F.367, C:T.371, C:L.375, C:F.497, C:F.497, C:A.499, B:F.522, B:F.522, B:F.522, B:L.526 Hydrogen bonds: C:N.500 Y01.25: 13 residues within 4Å: Chain C: F.522, C.525, L.526 Chain D: W.315, Y.316, F.364, F.367, T.371, L.375, L.496, F.497, A.499, N.500 11 PLIP interactions: 7 interactions with chain D, 4 interactions with chain C Hydrophobic interactions: D:F.367, D:T.371, D:L.375, D:F.497, D:F.497, D:A.499, C:F.522, C:F.522, C:F.522, C:L.526 Hydrogen bonds: D:N.500

4 x ZN: ZINC ION(Non-covalent)

ZN.5: 4 residues within 4Å: Chain A: H.172, C.176, C.178, C.181 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.172, A:C.176, A:C.178, A:C.181 ZN.12: 4 residues within 4Å: Chain B: H.172, C.176, C.178, C.181 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.172, B:C.176, B:C.178, B:C.181 ZN.19: 4 residues within 4Å: Chain C: H.172, C.176, C.178, C.181 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.172, C:C.176, C:C.178, C:C.181 ZN.26: 4 residues within 4Å: Chain D: H.172, C.176, C.178, C.181 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:H.172, D:C.176, D:C.178, D:C.181

4 x CA: CALCIUM ION(Non-covalent)

CA.6: 5 residues within 4Å: Chain A: E.418, E.421, N.436, D.439, R.492 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.418, A:D.439 CA.13: 5 residues within 4Å: Chain B: E.418, E.421, N.436, D.439, R.492 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.418, B:D.439 CA.20: 5 residues within 4Å: Chain C: E.418, E.421, N.436, D.439, R.492 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:E.418, C:D.439 CA.27: 5 residues within 4Å: Chain D: E.418, E.421, N.436, D.439, R.492 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:E.418, D:D.439

4 x YZY: (2S)-2-(hexadecanoyloxy)-3-hydroxypropyl (9Z)-octadec-9-enoate(Non-covalent)

YZY.7: 17 residues within 4Å: Chain A: L.514, L.521, Y.524, L.528, F.569, Q.573, F.576, W.577, V.579 Chain D: F.599, A.602, T.603, T.607, V.610, I.611, L.616 Ligands: PTY.2 13 PLIP interactions: 9 interactions with chain A, 4 interactions with chain D Hydrophobic interactions: A:L.514, A:L.521, A:Y.524, A:F.569, A:Q.573, A:F.576, A:V.579, D:V.610, D:V.610, D:I.611, D:L.616 Hydrogen bonds: A:Q.573, A:W.577 YZY.14: 17 residues within 4Å: Chain A: F.599, A.602, T.603, T.607, V.610, I.611, L.616 Chain B: L.514, L.521, Y.524, L.528, F.569, Q.573, F.576, W.577, V.579 Ligands: PTY.9 13 PLIP interactions: 9 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:L.514, B:L.521, B:Y.524, B:F.569, B:Q.573, B:F.576, B:V.579, A:V.610, A:V.610, A:I.611, A:L.616 Hydrogen bonds: B:Q.573, B:W.577 YZY.21: 17 residues within 4Å: Chain B: F.599, A.602, T.603, T.607, V.610, I.611, L.616 Chain C: L.514, L.521, Y.524, L.528, F.569, Q.573, F.576, W.577, V.579 Ligands: PTY.16 13 PLIP interactions: 9 interactions with chain C, 4 interactions with chain B Hydrophobic interactions: C:L.514, C:L.521, C:Y.524, C:F.569, C:Q.573, C:F.576, C:V.579, B:V.610, B:V.610, B:I.611, B:L.616 Hydrogen bonds: C:Q.573, C:W.577 YZY.28: 17 residues within 4Å: Chain C: F.599, A.602, T.603, T.607, V.610, I.611, L.616 Chain D: L.514, L.521, Y.524, L.528, F.569, Q.573, F.576, W.577, V.579 Ligands: PTY.23 13 PLIP interactions: 9 interactions with chain D, 4 interactions with chain C Hydrophobic interactions: D:L.514, D:L.521, D:Y.524, D:F.569, D:Q.573, D:F.576, D:V.579, C:V.610, C:V.610, C:I.611, C:L.616 Hydrogen bonds: D:Q.573, D:W.577

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Song, K. et al., Structural basis for human TRPC5 channel inhibition by two distinct inhibitors. Elife (2021)

Release Date

2021-03-31

Peptides

Short transient receptor potential channel 5: 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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Short transient receptor potential channel 5

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