Research workbench
Crystal structure of human lysophosphatidic acid receptor 1 in complex with ono-9910539
Analyse Crystal structure of human lysophosphatidic acid receptor 1 in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4Z35
- Type
- protein
- Length
- 382 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysophosphatidic acid receptor 1,SOLUBLE cytochrome B562
- UniProt
- Q92633, P0ABE7
- Ligands
- ON9, 1WV
- Pockets
- 6 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 79% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysophosphatidic acid receptor 1,SOLUBLE cytochrome B562 | protein | 382 | 79% helix, 1% strand | Q92633, P0ABE7 |
Ligands and binding sites
- ON9 · 3-{1-[(2S,3S)-3-(4-acetyl-3,5-dimethoxyphenyl)-2-(2,3-dihydro-1H-inden-2-ylmethyl)-3-hydroxypropyl]-4-(methoxycarbonyl)-1H-pyrrol-3-yl}propanoic acid · ligand · chains A
- 1WV · (2S)-2,3-dihydroxypropyl (7Z)-tetradec-7-enoate · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 432 | 0.83 | 0.91 | 43 | ON9 |
| 2 | 99 | 0.68 | 0.91 | 18 | empty |
| 3 | 152 | 0.68 | 0.88 | 25 | empty |
| 4 | 95 | 0.40 | 0.77 | 18 | empty |
| 5 | 69 | 0.35 | 0.77 | 15 | empty |
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 4Z35 · Crystal Structure of Human Lysophosphatidic Acid Receptor 1 in complex with ONO-9910539 · the same entry in another collection · chain A against A, TM-score 1.00
- Q92633 · AlphaFold monomer V2.0 prediction for lysophosphatidic acid receptor 1 (Q92633) · a predicted model of the same protein · chain A against A, TM-score 0.78
- 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 Q92633
- Every structure of UniProt P0ABE7
- Elsewhere: RCSB PDB 4Z35 · PDBe 4Z35 · UniProt Q92633 · UniProt P0ABE7
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