Research workbench
The crystal structure of human neuropeptide Y Y1 receptor with bms- 193885
Analyse The crystal structure of human neuropeptide Y Y1 receptor with bms- 193885 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ZBH
- Type
- protein
- Length
- 461 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neuropeptide Y receptor type 1,T4 LYSOZYME,NEUROPEPTIDE Y receptor type 1
- EC
- 3.2.1.17
- UniProt
- P25929, D9IEF7
- Ligands
- 9AF
- Pockets
- 5 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 71% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Neuropeptide Y receptor type 1,T4 LYSOZYME,NEUROPEPTIDE Y receptor type 1 (EC 3.2.1.17) | protein | 461 | 71% helix, 5% strand | P25929, D9IEF7 |
Ligands and binding sites
- 9AF · dimethyl 4-{3-[({3-[4-(3-methoxyphenyl)piperidin-1-yl]propyl}carbamoyl)amino]phenyl}-2,6-dimethyl-1,4-dihydropyridine-3,5-dicarboxylate · ligand · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 997 | 0.83 | 0.83 | 63 | 9AF |
| 2 | 193 | 0.47 | 0.75 | 34 | empty |
| 3 | 97 | 0.44 | 0.78 | 15 | empty |
| 4 | 69 | 0.37 | 0.77 | 14 | empty |
| 5 | 77 | 0.29 | 0.72 | 15 | empty |
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5ZBH · The Crystal Structure of Human Neuropeptide Y Y1 Receptor with BMS-193885 · the same entry in another collection · chain A against A, TM-score 1.00
- P25929 · AlphaFold monomer V2.0 prediction for neuropeptide Y receptor type 1 (P25929) · a predicted model of the same protein · chain A against A, TM-score 0.63
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 P25929
- Every structure of UniProt D9IEF7
- Elsewhere: RCSB PDB 5ZBH · PDBe 5ZBH · UniProt P25929 · UniProt D9IEF7
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