Research workbench
Crystal structure analysis of a OLEYL/OXADIAZOLE/PYRIDINE inhibitor bound to a humanized variant of fatty acid amide hydrolase
Analyse Crystal structure analysis of a OLEYL/OXADIAZOLE/PYRIDINE inhibitor bound to a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3K84
- Type
- protein
- Length
- 1,089 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fatty-acid amide hydrolase 1
- EC
- 3.5.1.-
- UniProt
- P97612
- Ligands
- K84, CL
- Pockets
- 9 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fatty-acid amide hydrolase 1 (EC 3.5.1.-) | protein | 546 | 47% helix, 13% strand | P97612 |
| B | Fatty-acid amide hydrolase 1 (EC 3.5.1.-) | protein | 543 | 46% helix, 13% strand | P97612 |
Ligands and binding sites
- K84 · (9Z)-1-(5-pyridin-2-yl-1,3,4-oxadiazol-2-yl)octadec-9-en-1-one · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1170 | 0.87 | 0.88 | 101 | CL |
| 2 | 299 | 0.79 | 0.90 | 44 | K84 |
| 3 | 301 | 0.79 | 0.90 | 45 | K84 |
| 4 | 152 | 0.44 | 0.76 | 25 | empty |
| 5 | 54 | 0.43 | 0.83 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1636 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 3K84 · Crystal Structure Analysis of a Oleyl/Oxadiazole/pyridine Inhibitor Bound to a Humanized… · the same entry in another collection · chain A against A, TM-score 1.00
- P97612 · AlphaFold monomer V2.0 prediction for fatty-acid amide hydrolase 1 (P97612) · a predicted model of the same protein · chain B against A, TM-score 1.00
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 P97612
- Elsewhere: RCSB PDB 3K84 · PDBe 3K84 · UniProt P97612
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