MolNFT v1 · #114412 · protein
Crystal structure of plasmodium falciparum dihydroorotate dehydrogenase bound with inhibitor DSM265
5BOO · Dihydroorotate dehydrogenase (quinone), mitochondrial: “Crystal structure of plasmodium falciparum dihydroorotate dehydrogenase bound with inhibitor DSM265”. X-ray diffraction, 3 ligands (D65, FMN, ORO), 8 pockets (best druggability…
- PDB
- 5BOO
- Type
- protein
- Length
- 747 residues
- Chains
- 2
- 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
- D65, FMN, ORO
- Pockets
- 8 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dihydroorotate dehydrogenase (quinone), mitochondrial (EC 1.3.5.2) | protein | 374 | 44% helix, 17% strand | Q08210 |
| B | Dihydroorotate dehydrogenase (quinone), mitochondrial (EC 1.3.5.2) | protein | 373 | 44% helix, 17% strand | Q08210 |
Ligands and binding sites
- D65 · 2-(1,1-difluoroethyl)-5-methyl-N-[4-(pentafluoro-lambda~6~-sulfanyl)phenyl][1,2,4]triazolo[1,5-a]pyrimidin-7-amine · ligand · 2 copies · chains A, B
- FMN · Flavin mononucleotide · ligand · 2 copies · chains A, B
- ORO · Orotic acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 337 | 0.86 | 0.95 | 55 | D65, FMN, ORO |
| 2 | 414 | 0.85 | 0.93 | 67 | D65, FMN, ORO |
| 3 | 549 | 0.65 | 0.77 | 76 | empty |
| 4 | 100 | 0.42 | 0.78 | 21 | empty |
| 5 | 157 | 0.41 | 0.73 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 646 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 5BOO · 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 5BOO · PDBe 5BOO · UniProt Q08210
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