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Crystal structure of human dihydroorotate dehydrogenase (DHODH) with brequinar analogue
Analyse Crystal structure of human dihydroorotate dehydrogenase (DHODH) with brequinar… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4JTU
- Type
- protein
- Length
- 365 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.9
- Source
- Homo sapiens
- Molecule
- Dihydroorotate dehydrogenase (quinone), mitochondrial
- EC
- 1.3.5.2
- UniProt
- Q02127
- Ligands
- FMN, ORO, DET, JTU, SO4
- Pockets
- 5 · best druggability 0.84
Structure
x-ray diffraction · resolution 1.9 · 1 distinct chain · 47% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dihydroorotate dehydrogenase (quinone), mitochondrial (EC 1.3.5.2) | protein | 365 | 47% helix, 16% strand | Q02127 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · chains A
- ORO · Orotic acid · ligand · chains A
- DET · Undecylamine-N,N-dimethyl-N-oxide · ligand · chains A
- JTU · 6-bromo-2-{4-[(2R)-butan-2-yl]phenyl}-3-methylquinoline-4-carboxylic acid · ligand · chains A
- SO4 · Sulfate ion · ion · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 413 | 0.84 | 0.91 | 57 | FMN, ORO, JTU |
| 2 | 95 | 0.51 | 0.83 | 20 | empty |
| 3 | 96 | 0.46 | 0.81 | 19 | DET |
| 4 | 83 | 0.41 | 0.79 | 18 | empty |
| 5 | 62 | 0.32 | 0.76 | 17 | empty |
Compared structures
- 4JTU · Crystal structure of human dihydroorotate dehydrogenase (dhodh) with brequinar analogue · the same entry in another collection · chain A against A, TM-score 1.00
- Q02127 · 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 Q02127
- Elsewhere: RCSB PDB 4JTU · PDBe 4JTU · UniProt Q02127
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