Research workbench
Crystal structure of the neurokinin 1 receptor in complex with the small molecule antagonist cp-99,994
Analyse Crystal structure of the neurokinin 1 receptor in complex with the small… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6HLL
- Type
- protein
- Length
- 469 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Substance-P RECEPTOR,GLGA glycogen SYNTHASE,SUBSTANCE-P receptor
- UniProt
- P25103, Q9V2J8
- Ligands
- GBK
- Pockets
- 4 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 69% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Substance-P RECEPTOR,GLGA glycogen SYNTHASE,SUBSTANCE-P receptor | protein | 469 | 69% helix, 9% strand | P25103, Q9V2J8 |
Ligands and binding sites
- GBK · (2~{S},3~{S})-~{N}-[(2-methoxyphenyl)methyl]-2-phenyl-piperidin-3-amine · ligand · 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 | 485 | 0.73 | 0.82 | 38 | GBK |
| 2 | 333 | 0.58 | 0.76 | 42 | empty |
| 3 | 167 | 0.46 | 0.75 | 27 | empty |
| 4 | 93 | 0.37 | 0.74 | 16 | empty |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6HLL · Crystal structure of the Neurokinin 1 receptor in complex with the small molecule… · the same entry in another collection · chain A against A, TM-score 1.00
- P25103 · AlphaFold monomer V2.0 prediction for substance-P receptor (P25103) · a predicted model of the same protein · chain A against A, TM-score 0.60
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 P25103
- Every structure of UniProt Q9V2J8
- Elsewhere: RCSB PDB 6HLL · PDBe 6HLL · UniProt P25103 · UniProt Q9V2J8
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