MolNFT v1 · #179398 · protein
Cryo-EM structure of human TRPV6 in complex with (4- PHENYLCYCLOHEXYL)PIPERAZINE inhibitor cis-22A
7K4B · Transient receptor potential cation channel subfamily V…: “Cryo-EM structure of human TRPV6 in complex with (4- PHENYLCYCLOHEXYL)PIPERAZINE inhibitor cis-22A”. Electron microscopy, 4 ligands (PCW, Y01, VUG), 20 pockets (best…
- PDB
- 7K4B
- Type
- protein
- Length
- 2,428 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
- PCW, Y01, VUG, CA
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 1 distinct chain · 48% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Transient receptor potential cation channel subfamily V member 6 | protein | 607 | 48% helix, 4% strand | Q9H1D0 |
Ligands and binding sites
- PCW · 1,2-dioleoyl-sn-glycero-3-phosphocholine · ligand · 48 copies · chains A, D, B, C
- Y01 · Cholesterol hemisuccinate · ligand · 8 copies · chains A, D, B, C
- VUG · 1-[cis-4-(3-methylphenyl)cyclohexyl]-4-(pyridin-3-yl) piperazine · ligand · 5 copies · chains A, B, D, C
- CA · Calcium ion · metal · 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, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 440 | 0.85 | 0.93 | 40 | CA |
| 2 | 255 | 0.80 | 0.92 | 22 | VUG |
| 3 | 1157 | 0.76 | 0.78 | 84 | VUG, Y01 |
| 4 | 1085 | 0.76 | 0.78 | 82 | VUG, Y01 |
| 5 | 1079 | 0.76 | 0.78 | 82 | VUG, Y01 |
Interfaces
6 interfaces between chains.
- C–D · 3684 Ų buried · 19 hydrogen bonds · protein-protein
- A–D · 3678 Ų buried · 22 hydrogen bonds · protein-protein
- B–C · 3668 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 3663 Ų buried · 20 hydrogen bonds · protein-protein
- B–D · 18 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7K4B · 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 0.98
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 7K4B · PDBe 7K4B · UniProt Q9H1D0
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