Research workbench
Crystal structure of plasmodium falciparum dihydroorotate dehydrogenase bound with inhibitor DSM784 (3-(1-(3-methyl-4-((6- (TRIFLUOROMETHYL)PYRIDIN-3-YL)METHYL)-1H-pyrrole-2-carboxamido) ethyl)-1H-pyrazole-5-carboxamide)
Analyse Crystal structure of plasmodium falciparum dihydroorotate dehydrogenase bound… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7L0K
- Type
- protein
- Length
- 752 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
- XE7, FMN, ORO
- Pockets
- 5 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dihydroorotate dehydrogenase (quinone), mitochondrial (EC 1.3.5.2) | protein | 381 | 44% helix, 16% strand | Q08210 |
| B | Dihydroorotate dehydrogenase (quinone), mitochondrial (EC 1.3.5.2) | protein | 371 | 44% helix, 17% strand | Q08210 |
Ligands and binding sites
- XE7 · 3-{(1R)-1-[(3-methyl-4-{[6-(trifluoromethyl)pyridin-3-yl]methyl}-1H-pyrrole-2-carbonyl)amino]ethyl}-1H-pyrazole-5-carboxamide · 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
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 538 | 0.83 | 0.89 | 72 | XE7, FMN, ORO |
| 2 | 890 | 0.83 | 0.85 | 95 | XE7, FMN, ORO |
| 3 | 310 | 0.55 | 0.75 | 25 | empty |
| 4 | 115 | 0.41 | 0.76 | 22 | empty |
| 5 | 110 | 0.38 | 0.75 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 486 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 7L0K · 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 B 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 Q08210
- Elsewhere: RCSB PDB 7L0K · PDBe 7L0K · UniProt Q08210
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