MolNFT v1 · #78653 · protein
Crystal structure of plasmodium falciparum dihydroorotate dehydrogenase bound with inhibitor DSM267
3SFK · Dihydroorotate dehydrogenase (quinone), mitochondrial: “Crystal structure of plasmodium falciparum dihydroorotate dehydrogenase bound with inhibitor DSM267”. X-ray diffraction, 3 ligands (D67, FMN, ORO), 4 pockets (best druggability…
- PDB
- 3SFK
- Type
- protein
- Length
- 368 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
- Q08210
- Ligands
- D67, FMN, ORO
- Pockets
- 4 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dihydroorotate dehydrogenase (quinone), mitochondrial (EC 1.3.5.2) | protein | 368 | 42% helix, 16% strand | Q08210 |
Ligands and binding sites
- D67 · 2-(1,1-difluoroethyl)-5-methyl-N-[4-(trifluoromethyl)phenyl][1,2,4]triazolo[1,5-a]pyrimidin-7-amine · ligand · chains A
- FMN · Flavin mononucleotide · ligand · chains A
- ORO · Orotic acid · ligand · 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 | 458 | 0.85 | 0.92 | 68 | D67, FMN, ORO |
| 2 | 94 | 0.39 | 0.77 | 27 | empty |
| 3 | 53 | 0.35 | 0.79 | 24 | empty |
| 4 | 57 | 0.30 | 0.76 | 15 | empty |
Compared structures
- 3SFK · Crystal structure of Plasmodium falciparum dihydroorotate dehydrogenase bound with… · the same entry in another collection · chain A against A, TM-score 1.00
- Q08210 · AlphaFold monomer V2.0 prediction for dihydroorotate dehydrogenase (quinone)… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q08210
- Elsewhere: RCSB PDB 3SFK · PDBe 3SFK · UniProt Q08210
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