MolNFT v1 · #150112 · protein
Human dihydroorotate dehydrogenase in complex with class III histone deacetylase inhibitor
6GK0 · Dihydroorotate dehydrogenase (quinone), mitochondrial: “Human dihydroorotate dehydrogenase in complex with class III histone deacetylase inhibitor”. X-ray diffraction, 6 ligands (FMN, DOR, DDQ), 4 pockets (best druggability 0.83).…
- PDB
- 6GK0
- Type
- protein
- Length
- 363 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, DOR, DDQ, F1W, SO4, CL
- Pockets
- 4 · best druggability 0.83
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 | 363 | 46% helix, 17% strand | Q02127 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · chains A
- DOR · (4S)-2,6-dioxohexahydropyrimidine-4-carboxylic acid · ligand · chains A
- DDQ · Decylamine-N,N-dimethyl-N-oxide · ligand · chains A
- F1W · 4-~{tert}-butyl-~{N}-[[4-[5-(dimethylamino) pentanoylamino]phenyl]carbamothioyl]benzamide · ligand · chains A
- SO4 · Sulfate ion · ion · 5 copies · chains A
- CL · Chloride ion · ion · chains A
- ACY · Acetic acid · additive · 4 copies · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 404 | 0.83 | 0.91 | 63 | FMN, DOR, F1W |
| 2 | 137 | 0.48 | 0.79 | 25 | ACY |
| 3 | 88 | 0.42 | 0.79 | 18 | DDQ |
| 4 | 106 | 0.42 | 0.78 | 25 | ACY |
Compared structures
- 6GK0 · Human dihydroorotate dehydrogenase in complex with class III histone deacetylase inhibitor · 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 6GK0 · PDBe 6GK0 · UniProt Q02127
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