Research workbench
Human dihydroorotate dehydrogenase bound to napthyridine inhibitor 46
Analyse Human dihydroorotate dehydrogenase bound to napthyridine inhibitor 46 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6CJG
- Type
- protein
- Length
- 354 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, F51, ZWI, SO4
- Pockets
- 6 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dihydroorotate dehydrogenase (quinone), mitochondrial (EC 1.3.5.2) | protein | 354 | 46% helix, 17% strand | Q02127 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · chains A
- ORO · Orotic acid · ligand · chains A
- F51 · 2-([1,1'-biphenyl]-4-yl)-3-methyl-1,7-naphthyridine-4-carboxylic acid · ligand · chains A
- ZWI · 3-[decyl(dimethyl)ammonio]propane-1-sulfonate · ligand · chains A
- SO4 · Sulfate ion · ion · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 454 | 0.85 | 0.92 | 63 | FMN, ORO, F51 |
| 2 | 162 | 0.59 | 0.83 | 38 | empty |
| 3 | 108 | 0.48 | 0.80 | 19 | empty |
| 4 | 69 | 0.39 | 0.79 | 15 | empty |
| 5 | 72 | 0.37 | 0.77 | 16 | empty |
Compared structures
- 6CJG · Human dihydroorotate dehydrogenase bound to napthyridine inhibitor 46 · 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 6CJG · PDBe 6CJG · UniProt Q02127
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