Research workbench
Enantiomer-specific binding of the potent antinociceptive agent sbfi- 26 to anandamide transporters FABP7
Analyse Enantiomer-specific binding of the potent antinociceptive agent sbfi- 26 to… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5URA
- Type
- protein
- Length
- 537 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fatty acid-binding protein, brain
- UniProt
- O15540
- Ligands
- 8KS, SO4
- Pockets
- 8 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 16% helix, 57% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Fatty acid-binding protein, brain | protein | 134 | 16% helix, 57% strand | O15540 |
| B | Fatty acid-binding protein, brain | protein | 135 | 16% helix, 56% strand | O15540 |
Ligands and binding sites
- 8KS · (1S,2S,3S,4S)-3-{[(naphthalen-1-yl)oxy]carbonyl}-2,4-diphenylcyclobutane-1-carboxylic acid · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 395 | 0.85 | 0.93 | 35 | 8KS |
| 2 | 390 | 0.85 | 0.93 | 36 | 8KS |
| 3 | 398 | 0.85 | 0.93 | 38 | 8KS |
| 4 | 388 | 0.84 | 0.93 | 35 | 8KS |
| 5 | 327 | 0.68 | 0.82 | 40 | empty |
Interfaces
5 interfaces between chains.
- B–D · 628 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 444 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 247 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 75 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 17 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5URA · Enantiomer-Specific Binding of the Potent Antinociceptive Agent SBFI-26 to Anandamide… · the same entry in another collection · chain D against D, TM-score 1.00
- O15540 · AlphaFold monomer V2.0 prediction for fatty acid-binding protein, brain (O15540) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 O15540
- Elsewhere: RCSB PDB 5URA · PDBe 5URA · UniProt O15540
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