MolNFT v1 · #54193 · protein
Crystal structure of N-((2S)-5-(6-fluoro-3-pyridinyl)-2,3- dihydro-1H-inden-2-yl)-2-propanesulfonamide in complex with the ligand binding domain of the human GLUA2 receptor
2XHD · Glutamate receptor 2: “Crystal structure of N-((2S)-5-(6-fluoro-3-pyridinyl)-2,3- dihydro-1H-inden-2-yl)-2-propanesulfonamide in…”. X-ray diffraction, 3 ligands (GLU, 7T9, SO4), 4 pockets (best druggability 0.79). MolNFT v1 #54193…
- PDB
- 2XHD
- Type
- protein
- Length
- 515 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate receptor 2
- UniProt
- P42262
- Ligands
- GLU, 7T9, SO4
- Pockets
- 4 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamate receptor 2 | protein | 260 | 37% helix, 21% strand | P42262 |
| B | Glutamate receptor 2 | protein | 255 | 38% helix, 21% strand | P42262 |
Ligands and binding sites
- GLU · Glutamic acid · ligand · 2 copies · chains A, B
- 7T9 · N-[(2S)-5-(6-fluoro-3-pyridinyl)-2,3-dihydro-1H-inden-2-yl]-2-propanesulfonamide · ligand · chains A, B
- SO4 · Sulfate ion · ion · 5 copies · chains A, B
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 | 828 | 0.79 | 0.82 | 92 | 7T9, SO4 |
| 2 | 98 | 0.54 | 0.85 | 21 | empty |
| 3 | 77 | 0.40 | 0.79 | 18 | SO4 |
| 4 | 97 | 0.38 | 0.76 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 873 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 2XHD · Crystal structure of N-((2S)-5-(6-fluoro-3-pyridinyl)-2,3-dihydro-1H… · the same entry in another collection · chain A against A, TM-score 1.00
- P42262 · AlphaFold monomer V2.0 prediction for glutamate receptor 2 (P42262) · 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 P42262
- Elsewhere: RCSB PDB 2XHD · PDBe 2XHD · UniProt P42262
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