MolNFT v1 · #138427 · protein
Structure of the sodium-bound human D4 dopamine receptor in complex with nemonapride
5WIV · D(4) dopamine receptor, soluble cytochrome B562 chimera: “Structure of the sodium-bound human D4 dopamine receptor in complex with nemonapride”. X-ray diffraction, 4 ligands (OLA, AQD, NA), 5 pockets (best druggability 0.77). MolNFT…
- PDB
- 5WIV
- Type
- protein
- Length
- 379 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D(4) dopamine receptor, soluble cytochrome B562 chimera
- UniProt
- P21917, P0ABE7
- Ligands
- OLA, AQD, NA, PO4
- Pockets
- 5 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 79% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | D(4) dopamine receptor, soluble cytochrome B562 chimera | protein | 379 | 79% helix, 1% strand | P21917, P0ABE7 |
Ligands and binding sites
- OLA · Oleic acid · ligand · 8 copies · chains A
- AQD · Nemonapride · ligand · chains A
- NA · Sodium ion · metal · chains A
- PO4 · Phosphate ion · ion · 5 copies · chains A
- PEG · Di(hydroxyethyl)ether · additive · 9 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 437 | 0.77 | 0.86 | 45 | AQD |
| 2 | 472 | 0.62 | 0.76 | 38 | PO4 |
| 3 | 183 | 0.56 | 0.79 | 19 | empty |
| 4 | 62 | 0.38 | 0.79 | 14 | OLA |
| 5 | 57 | 0.27 | 0.73 | 15 | empty |
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5WIV · Structure of the sodium-bound human D4 Dopamine receptor in complex with Nemonapride · the same entry in another collection · chain A against A, TM-score 1.00
- P21917 · AlphaFold monomer V2.0 prediction for D(4) dopamine receptor (P21917) · a predicted model of the same protein · chain A against A, TM-score 0.71
- P0ABE7 · AlphaFold monomer V2.0 prediction for soluble cytochrome B562 (P0ABE7) · a predicted model of the same protein · chain A against A, TM-score 0.27
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 P21917
- Every structure of UniProt P0ABE7
- Elsewhere: RCSB PDB 5WIV · PDBe 5WIV · UniProt P21917 · UniProt P0ABE7
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