MolNFT v1 · #167994 · protein
Crystal structure of the melanocortin-4 receptor (MC4R) in complex with SHU9119
6W25 · Melanocortin receptor 4,GLGA glycogen SYNTHASE,MELANOCORTIN…: “Crystal structure of the melanocortin-4 receptor (MC4R) in complex with SHU9119”. X-ray diffraction, 4 ligands (OLA, ACE, CA), 5 pockets (best druggability 0.60). MolNFT…
- PDB
- 6W25
- Type
- protein
- Length
- 475 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Melanocortin receptor 4,GLGA glycogen SYNTHASE,MELANOCORTIN receptor 4; SHU9119
- UniProt
- P32245, Q9V2J8
- Ligands
- OLA, ACE, CA, NH2
- Pockets
- 5 · best druggability 0.60
Structure
x-ray diffraction · 2 distinct chains · 71% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Melanocortin receptor 4,GLGA glycogen SYNTHASE,MELANOCORTIN receptor 4 | protein | 468 | 72% helix, 7% strand | P32245, Q9V2J8 |
| B | SHU9119 | protein | 7 | 0% helix, 0% strand | — |
Ligands and binding sites
- OLA · Oleic acid · ligand · 8 copies · chains A
- ACE · Acetyl group · ligand · chains B
- CA · Calcium ion · metal · chains A, B
- NH2 · Amino group · ion · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 209 | 0.60 | 0.80 | 24 | OLA |
| 2 | 157 | 0.46 | 0.76 | 27 | empty |
| 3 | 113 | 0.45 | 0.78 | 25 | empty |
| 4 | 66 | 0.28 | 0.73 | 14 | empty |
| 5 | 50 | 0.25 | 0.74 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 820 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 modified, 1 covalent, 1 disulfide, 1 isopeptide (nonstandard, covalent ligand, disulfide, isopeptide, alkylation).
Compared structures
- 6W25 · Crystal structure of the Melanocortin-4 Receptor (MC4R) in complex with SHU9119 · the same entry in another collection · chain A against A, TM-score 1.00
- P32245 · AlphaFold monomer V2.0 prediction for melanocortin receptor 4 (P32245) · a predicted model of the same protein · chain A against A, TM-score 0.55
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 P32245
- Every structure of UniProt Q9V2J8
- Elsewhere: RCSB PDB 6W25 · PDBe 6W25 · UniProt P32245 · UniProt Q9V2J8
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