MolNFT v1 · #54703 · protein
Crystal structure of N,N-dimethyl-4-(3-(trifluoromethyl)-4, 5,6,7-tetrahydro-1H-indazol-1-YL)BENZAMIDE in complex with the ligand binding domain of the rat GLUA2 receptor and glutamate at 2.2A resolution.
2XX8 · Glutamate receptor 2: “Crystal structure of N,N-dimethyl-4-(3-(trifluoromethyl)-4, 5,6,7-tetrahydro-1H-indazol-1-YL)BENZAMIDE in…”. X-ray diffraction, 4 ligands (GLU, 1NE, ZN), 5 pockets (best druggability 0.83). MolNFT v1 #54703 on…
- PDB
- 2XX8
- Type
- protein
- Length
- 778 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate receptor 2
- UniProt
- P19491
- Ligands
- GLU, 1NE, ZN, SO4
- Pockets
- 5 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Glutamate receptor 2 | protein | 259 | 39% helix, 21% strand | P19491 |
| C | Glutamate receptor 2 | protein | 260 | 38% helix, 21% strand | P19491 |
Ligands and binding sites
- GLU · Glutamic acid · ligand · 3 copies · chains A, B, C
- 1NE · N,N-dimethyl-4-[3-(trifluoromethyl)-4,5,6,7-tetrahydro-1H-indazol-1-yl]benzamide · ligand · 2 copies · chains A, C, B
- ZN · Zinc ion · metal · 5 copies · chains A, B, C
- SO4 · Sulfate ion · ion · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 952 | 0.83 | 0.84 | 126 | 1NE |
| 2 | 271 | 0.58 | 0.78 | 33 | empty |
| 3 | 183 | 0.43 | 0.74 | 27 | empty |
| 4 | 68 | 0.37 | 0.78 | 21 | empty |
| 5 | 53 | 0.34 | 0.78 | 22 | empty |
Interfaces
3 interfaces between chains.
- A–C · 853 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 240 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 52 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
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 P19491
- Elsewhere: RCSB PDB 2XX8 · PDBe 2XX8 · UniProt P19491
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