Research workbench
Structure of human TRPC5 in complex with clemizole
Analyse Structure of human TRPC5 in complex with clemizole in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7D4P
- Type
- protein
- Length
- 2,676 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Short transient receptor potential channel 5
- UniProt
- Q9UL62
- Ligands
- GX0, PTY, POV, Y01, YZY, ZN, CA
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 1 distinct chain · 68% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Short transient receptor potential channel 5 | protein | 669 | 68% helix, 1% strand | Q9UL62 |
Ligands and binding sites
- GX0 · 1-[(4-chlorophenyl)methyl]-2-(pyrrolidin-1-ylmethyl) benzimidazole · ligand · 4 copies · chains A, B, C, D
- PTY · Phosphatidylethanolamine · ligand · 4 copies · chains A, D, B, C
- POV · (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate · ligand · 4 copies · chains A, D, B, C
- Y01 · Cholesterol hemisuccinate · ligand · 4 copies · chains A, D, B, C
- YZY · (2S)-2-(hexadecanoyloxy)-3-hydroxypropyl (9Z)-octadec-9-enoate · ligand · 4 copies · chains A, D, B, C
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 967 | 0.87 | 0.88 | 101 | empty |
| 2 | 1145 | 0.84 | 0.85 | 102 | empty |
| 3 | 963 | 0.83 | 0.84 | 78 | GX0, PTY, CA |
| 4 | 1057 | 0.82 | 0.83 | 103 | empty |
| 5 | 990 | 0.82 | 0.83 | 82 | empty |
Interfaces
6 interfaces between chains.
- A–B · 5121 Ų buried · 34 hydrogen bonds · protein-protein
- B–C · 5119 Ų buried · 34 hydrogen bonds · protein-protein
- C–D · 5113 Ų buried · 34 hydrogen bonds · protein-protein
- A–D · 5107 Ų buried · 34 hydrogen bonds · protein-protein
- A–C · 95 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q9UL62
- Elsewhere: RCSB PDB 7D4P · PDBe 7D4P · UniProt Q9UL62
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