Research workbench
Crystal structure of plasmodium falciparum dihydroorotate dehydrogenase bound with inhibitor DSM697 (3-methyl-N-(1-(5- methylisoxazol-3-YL)ETHYL)-4-(6-(trifluoromethyl)-1H-indol-3-yl)-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
- 7KYY
- Type
- protein
- Length
- 1,483 residues
- Chains
- 4
- 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
- XCD, FMN, ORO
- Pockets
- 15 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 43% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dihydroorotate dehydrogenase (quinone), mitochondrial (EC 1.3.5.2) | protein | 376 | 43% helix, 17% strand | Q08210 |
| B | Dihydroorotate dehydrogenase (quinone), mitochondrial (EC 1.3.5.2) | protein | 364 | 44% helix, 18% strand | Q08210 |
| C | Dihydroorotate dehydrogenase (quinone), mitochondrial (EC 1.3.5.2) | protein | 372 | 43% helix, 18% strand | Q08210 |
| D | Dihydroorotate dehydrogenase (quinone), mitochondrial (EC 1.3.5.2) | protein | 371 | 43% helix, 17% strand | Q08210 |
Ligands and binding sites
- XCD · 3-methyl-N-[(1R)-1-(5-methyl-1,2-oxazol-3-yl)ethyl]-4-[6-(trifluoromethyl)-1H-indol-3-yl]-1H-pyrrole-2-carboxamide · ligand · 4 copies · chains A, B, C, D
- FMN · Flavin mononucleotide · ligand · 4 copies · chains A, B, C, D
- ORO · Orotic acid · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 454 | 0.84 | 0.91 | 63 | XCD, FMN, ORO |
| 2 | 438 | 0.83 | 0.91 | 61 | XCD, FMN, ORO |
| 3 | 407 | 0.83 | 0.91 | 61 | XCD, FMN, ORO |
| 4 | 446 | 0.83 | 0.90 | 65 | XCD, FMN, ORO |
| 5 | 998 | 0.72 | 0.76 | 73 | empty |
Interfaces
5 interfaces between chains.
- A–B · 788 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 778 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 471 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 451 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 122 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 7KYY · Crystal structure of Plasmodium falciparum dihydroorotate dehydrogenase bound with… · the same entry in another collection · chain D against D, 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 7KYY · PDBe 7KYY · UniProt Q08210
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