MolNFT v1 · #116468 · protein
Crystal structure of plasmodium falciparum dihydroorotate dehydrogenase bound with inhibitor DSM59
5DEL · Dihydroorotate dehydrogenase (quinone), mitochondrial: “Crystal structure of plasmodium falciparum dihydroorotate dehydrogenase bound with inhibitor DSM59”. X-ray diffraction, 3 ligands (FMN, ORO, D59), 2 pockets (best druggability…
- PDB
- 5DEL
- Type
- protein
- Length
- 374 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
- FMN, ORO, D59
- Pockets
- 2 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dihydroorotate dehydrogenase (quinone), mitochondrial (EC 1.3.5.2) | protein | 374 | 45% helix, 16% strand | Q08210 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · chains A
- ORO · Orotic acid · ligand · chains A
- D59 · N-(3,5-dichlorophenyl)-2-methyl-3-nitrobenzamide · ligand · chains A
- GOL · Glycerol · additive · 2 copies · chains A
- LDA · Lauryl dimethylamine-N-oxide · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 437 | 0.84 | 0.91 | 69 | FMN, ORO, D59 |
| 2 | 75 | 0.39 | 0.78 | 19 | empty |
Compared structures
- 5DEL · 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 5DEL · PDBe 5DEL · UniProt Q08210
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