MolNFT v2 · #220639 · protein
CDPPB-bound inactive mGlu5
8T6J · Metabotropic glutamate receptor 5: “CDPPB-bound inactive mGlu5”. Electron microscopy at 3.5, 1 ligand (YKU), 16 pockets (best druggability 0.82). MolNFT v2 #220639 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 8T6J
- Type
- protein
- Length
- 1,534 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.5
- Source
- Homo sapiens
- Molecule
- Metabotropic glutamate receptor 5
- UniProt
- P41594
- Ligands
- YKU
- Pockets
- 16 · best druggability 0.82
Structure
electron microscopy · resolution 3.5 · 1 distinct chain · 45% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A | Metabotropic glutamate receptor 5 | protein | 767 | 45% helix, 14% strand | P41594 |
Ligands and binding sites
- YKU · 3-cyano-N-(1,3-diphenyl-1H-pyrazol-5-yl)benzamide · ligand · 2 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 301 | 0.82 | 0.92 | 49 | YKU |
| 2 | 274 | 0.81 | 0.92 | 36 | YKU |
| 3 | 196 | 0.68 | 0.86 | 32 | empty |
| 4 | 324 | 0.67 | 0.81 | 41 | empty |
| 5 | 204 | 0.66 | 0.85 | 32 | empty |
Interfaces
1 interface between chains.
- B–A · 552 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide (disulfide).
Compared structures
- P41594 · AlphaFold monomer V2.0 prediction for metabotropic glutamate receptor 5 (P41594) · a predicted model of the same protein · chain B against A, TM-score 0.87
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 P41594
- Elsewhere: RCSB PDB 8T6J · PDBe 8T6J · UniProt P41594
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