Research workbench
Crystal structure of 1-(4-(1-PYRROLIDINYLCARBONYL)PHENYL)-3- (trifluoromethyl)-4,5,6,7-tetrahydro-1H-indazole in complex with the ligand binding domain of the rat GLUA2 receptor and glutamate at 2.2A resolution.
Analyse Crystal structure of 1-(4-(1-PYRROLIDINYLCARBONYL)PHENYL)-3… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2XX7
- Type
- protein
- Length
- 784 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate receptor 2
- UniProt
- P19491
- Ligands
- GLU, 1ND, ZN, SO4
- Pockets
- 7 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Glutamate receptor 2 | protein | 262 | 39% helix, 21% strand | P19491 |
| C | Glutamate receptor 2 | protein | 260 | 38% helix, 23% strand | P19491 |
Ligands and binding sites
- GLU · Glutamic acid · ligand · 3 copies · chains A, B, C
- 1ND · 1-[4-(1-pyrrolidinylcarbonyl)phenyl]-3-(trifluoromethyl)-4,5,6,7-tetrahydro-1H-indazole · 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
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 688 | 0.81 | 0.85 | 104 | 1ND |
| 2 | 513 | 0.72 | 0.81 | 60 | SO4 |
| 3 | 271 | 0.57 | 0.78 | 29 | empty |
| 4 | 95 | 0.40 | 0.76 | 21 | empty |
| 5 | 74 | 0.36 | 0.77 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–C · 898 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 288 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 49 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 2XX7 · Crystal structure of 1-(4-(1-pyrrolidinylcarbonyl)phenyl)-3-(trifluoromethyl)-4,5,6,7-tetr… · the same entry in another collection · chain C against C, TM-score 1.00
- P19491 · AlphaFold monomer V2.0 prediction for glutamate receptor 2 (P19491) · 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 P19491
- Elsewhere: RCSB PDB 2XX7 · PDBe 2XX7 · UniProt P19491
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.