Research workbench
Crystal structure of human GPR40 bound to allosteric agonist tak-875
Analyse Crystal structure of human GPR40 bound to allosteric agonist tak-875 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4PHU
- Type
- protein
- Length
- 434 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Free fatty acid receptor 1,LYSOZYME
- EC
- 3.2.1.17
- UniProt
- O14842, P00720
- Ligands
- 2YB
- Pockets
- 4 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 71% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Free fatty acid receptor 1,LYSOZYME (EC 3.2.1.17) | protein | 434 | 71% helix, 4% strand | O14842, P00720 |
Ligands and binding sites
- 2YB · [(3S)-6-({2',6'-dimethyl-4'-[3-(methylsulfonyl)propoxy]biphenyl-3-yl}methoxy)-2,3-dihydro-1-benzofuran-3-yl]acetic acid · ligand · chains A
- OLC · (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · additive · 5 copies · chains A
- 1PE · Pentaethylene glycol · additive · chains A
- DMS · Dimethyl sulfoxide · additive · 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 | 110 | 0.71 | 0.92 | 22 | 2YB |
| 2 | 179 | 0.53 | 0.79 | 35 | empty |
| 3 | 204 | 0.47 | 0.74 | 27 | empty |
| 4 | 66 | 0.31 | 0.74 | 17 | OLC |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 4PHU · Crystal structure of Human GPR40 bound to allosteric agonist TAK-875 · the same entry in another collection · chain A against A, TM-score 1.00
- O14842 · AlphaFold monomer V2.0 prediction for free fatty acid receptor 1 (O14842) · a predicted model of the same protein · chain A against A, TM-score 0.62
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 O14842
- Every structure of UniProt P00720
- Elsewhere: RCSB PDB 4PHU · PDBe 4PHU · UniProt O14842 · UniProt P00720
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