MolNFT v1 · #115329 · protein
Structure of the human class C GPCR metabotropic glutamate receptor 5 transmembrane domain in complex with the negative allosteric modulator 3-chloro-4-fluoro-5-[6-(1H-pyrazol-1-YL)PYRIMIDIN-4- YL]BENZONITRILE
5CGC · Metabotropic glutamate receptor 5,ENDOLYSIN,METABOTROPIC…: “Structure of the human class C GPCR metabotropic glutamate receptor 5 transmembrane domain in complex with…”. X-ray diffraction, 2 ligands (OLA, 51D), 3 pockets (best…
- PDB
- 5CGC
- Type
- protein
- Length
- 409 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Metabotropic glutamate receptor 5,ENDOLYSIN,METABOTROPIC glutamate receptor 5
- EC
- 3.2.1.17
- UniProt
- P41594, P00720
- Ligands
- OLA, 51D
- Pockets
- 3 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 72% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Metabotropic glutamate receptor 5,ENDOLYSIN,METABOTROPIC glutamate receptor 5 (EC 3.2.1.17) | protein | 409 | 72% helix, 3% strand | P41594, P00720 |
Ligands and binding sites
- OLA · Oleic acid · ligand · 4 copies · chains A
- 51D · 3-chloro-4-fluoro-5-[6-(1H-pyrazol-1-yl)pyrimidin-4-yl]benzonitrile · ligand · chains A
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 246 | 0.78 | 0.91 | 42 | MES, 51D |
| 2 | 56 | 0.71 | 0.98 | 18 | empty |
| 3 | 465 | 0.67 | 0.79 | 45 | empty |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5CGC · Structure of the human class C GPCR metabotropic glutamate receptor 5 transmembrane… · the same entry in another collection · chain A against A, TM-score 1.00
- P41594 · AlphaFold monomer V2.0 prediction for metabotropic glutamate receptor 5 (P41594) · a predicted model of the same protein · chain A against A, TM-score 0.58
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
- Every structure of UniProt P00720
- Elsewhere: RCSB PDB 5CGC · PDBe 5CGC · UniProt P41594 · UniProt P00720
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