Research workbench
Dhodh in complex with ligand 19
Analyse Dhodh in complex with ligand 19 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8DHG
- Type
- protein
- Length
- 359 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydroorotate dehydrogenase (quinone), mitochondrial
- EC
- 1.3.5.2
- UniProt
- Q02127
- Ligands
- FMN, ORO, T78, SO4
- Pockets
- 5 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dihydroorotate dehydrogenase (quinone), mitochondrial (EC 1.3.5.2) | protein | 359 | 47% helix, 17% strand | Q02127 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · chains A
- ORO · Orotic acid · ligand · chains A
- T78 · (6M)-N-(2-chloro-4-methylpyridin-3-yl)-6-[4-ethyl-3-(hydroxymethyl)-5-oxo-4,5-dihydro-1H-1,2,4-triazol-1-yl]-5-fluoro-2-{[(2S)-1,1,1-trifluoropropan-2-yl]oxy}pyridine-3-carboxamide · ligand · chains A
- SO4 · Sulfate ion · ion · 2 copies · chains A
- ACT · Acetate ion · additive · 2 copies · chains A
- GOL · Glycerol · additive · chains A
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 | 631 | 0.79 | 0.84 | 79 | FMN, ORO, T78 |
| 2 | 161 | 0.64 | 0.85 | 28 | empty |
| 3 | 91 | 0.43 | 0.79 | 18 | SO4 |
| 4 | 94 | 0.41 | 0.78 | 18 | ACT |
| 5 | 85 | 0.36 | 0.75 | 16 | empty |
Compared structures
- 8DHG · Dhodh in complex with ligand 19 · the same entry in another collection · chain A against A, TM-score 1.00
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 Q02127
- Elsewhere: RCSB PDB 8DHG · PDBe 8DHG · UniProt Q02127
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.