Research workbench
Structure of the human D4 dopamine receptor in complex with nemonapride
Analyse Structure of the human D4 dopamine receptor in complex with nemonapride in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5WIU
- Type
- protein
- Length
- 373 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, PO4
- Pockets
- 4 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 80% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | D(4) dopamine receptor, soluble cytochrome B562 chimera | protein | 373 | 80% helix, 1% strand | P21917, P0ABE7 |
Ligands and binding sites
- OLA · Oleic acid · ligand · 9 copies · chains A
- AQD · Nemonapride · ligand · chains A
- PO4 · Phosphate ion · ion · 3 copies · chains A
- PEG · Di(hydroxyethyl)ether · additive · 9 copies · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 434 | 0.77 | 0.85 | 43 | AQD |
| 2 | 653 | 0.69 | 0.77 | 58 | PO4, GOL |
| 3 | 57 | 0.38 | 0.79 | 13 | OLA |
| 4 | 59 | 0.27 | 0.72 | 15 | OLA |
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5WIU · Structure of the 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 0.28
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 5WIU · PDBe 5WIU · UniProt P21917 · UniProt P0ABE7
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