Research workbench
Crystal structure of plasmodium falciparum dihydroorotate dehydrogenase bound with inhibitor DSM778 (3-methyl-N-(1-(5-methyl- 1H-pyrazol-3-YL)ETHYL)-4-(1-(6-(TRIFLUOROMETHYL)PYRIDIN-3-yl) cyclopropyl)-1H-pyrrole-2-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
- 7KZY
- Type
- protein
- Length
- 762 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
- XCM, FMN, ORO
- Pockets
- 7 · best druggability 0.82
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 | 384 | 44% helix, 16% strand | Q08210 |
| B | Dihydroorotate dehydrogenase (quinone), mitochondrial (EC 1.3.5.2) | protein | 378 | 45% helix, 16% strand | Q08210 |
Ligands and binding sites
- XCM · 3-methyl-N-[(1R)-1-(5-methyl-1H-pyrazol-3-yl)ethyl]-4-{1-[6-(trifluoromethyl)pyridin-3-yl]cyclopropyl}-1H-pyrrole-2-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
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 867 | 0.82 | 0.84 | 100 | XCM, FMN, ORO |
| 2 | 504 | 0.81 | 0.87 | 70 | XCM, FMN, ORO |
| 3 | 297 | 0.54 | 0.75 | 22 | empty |
| 4 | 121 | 0.43 | 0.77 | 23 | empty |
| 5 | 86 | 0.40 | 0.78 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 488 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 7KZY · 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 0.98
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 7KZY · PDBe 7KZY · UniProt Q08210
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