Research workbench
Cryo-EM structure of human TRPV6 in complex with (4- PHENYLCYCLOHEXYL)PIPERAZINE inhibitor 3OG
Analyse Cryo-EM structure of human TRPV6 in complex with (4… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7K4D
- Type
- protein
- Length
- 2,448 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transient receptor potential cation channel subfamily V member 6
- UniProt
- Q9H1D0
- Ligands
- VUM, CA
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 1 distinct chain · 50% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Transient receptor potential cation channel subfamily V member 6 | protein | 612 | 50% helix, 3% strand | Q9H1D0 |
Ligands and binding sites
- VUM · 5-[(4-{trans-4-hydroxy-4-[3-(trifluoromethyl) phenyl]cyclohexyl}piperazin-1-yl)methyl]pyridin-2(1H)-one · ligand · 5 copies · chains A, B, C, D
- CA · Calcium ion · metal · 2 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 | 419 | 0.84 | 0.92 | 43 | CA |
| 2 | 116 | 0.73 | 0.93 | 22 | empty |
| 3 | 195 | 0.72 | 0.88 | 24 | VUM |
| 4 | 120 | 0.71 | 0.92 | 28 | empty |
| 5 | 117 | 0.71 | 0.92 | 27 | empty |
Interfaces
6 interfaces between chains.
- B–C · 3764 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 3698 Ų buried · 20 hydrogen bonds · protein-protein
- A–D · 3694 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 3677 Ų buried · 19 hydrogen bonds · protein-protein
- B–D · 52 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7K4D · Cryo-EM structure of human TRPV6 in complex with (4- phenylcyclohexyl)piperazine… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9H1D0 · AlphaFold monomer V2.0 prediction for transient receptor potential cation channel… · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q9H1D0
- Elsewhere: RCSB PDB 7K4D · PDBe 7K4D · UniProt Q9H1D0
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