MolNFT v1 · #191385 · protein
Dhodh in complex with ligand 11
8DHF · Dihydroorotate dehydrogenase (quinone), mitochondrial: “Dhodh in complex with ligand 11”. X-ray diffraction, 4 ligands (FMN, ORO, T6L), 5 pockets (best druggability 0.80). MolNFT v1 #191385 on GenesisL1: 3D structure, binding sites…
- PDB
- 8DHF
- Type
- protein
- Length
- 355 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, T6L, SO4
- Pockets
- 5 · best druggability 0.80
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 | 355 | 46% helix, 17% strand | Q02127 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · chains A
- ORO · Orotic acid · ligand · chains A
- T6L · (6M)-N-(2-chloro-6-fluorophenyl)-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 · 5 copies · chains A
- GOL · Glycerol · additive · 8 copies · chains A
- ACT · Acetate ion · additive · 4 copies · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 602 | 0.80 | 0.85 | 73 | FMN, ORO, T6L |
| 2 | 92 | 0.46 | 0.81 | 17 | GOL |
| 3 | 102 | 0.42 | 0.78 | 19 | ACT, SO4 |
| 4 | 76 | 0.38 | 0.77 | 15 | empty |
| 5 | 70 | 0.31 | 0.74 | 15 | empty |
Compared structures
- 8DHF · Dhodh in complex with ligand 11 · 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 8DHF · PDBe 8DHF · UniProt Q02127
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