MolNFT v1 · #111270 · protein
Crystal structure of human dihydroorotate dehydrogenase (dhodh) with NO.33 compound
4YLW · Dihydroorotate dehydrogenase (quinone), mitochondrial: “Crystal structure of human dihydroorotate dehydrogenase (dhodh) with NO.33 compound”. X-ray diffraction, 4 ligands (52Y, FMN, ORO), 4 pockets (best druggability 0.85). MolNFT…
- PDB
- 4YLW
- Type
- protein
- Length
- 364 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydroorotate dehydrogenase (quinone), mitochondrial
- EC
- 1.3.5.2
- UniProt
- Q02127
- Ligands
- 52Y, FMN, ORO, SO4
- Pockets
- 4 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dihydroorotate dehydrogenase (quinone), mitochondrial (EC 1.3.5.2) | protein | 364 | 46% helix, 16% strand | Q02127 |
Ligands and binding sites
- 52Y · methyl (2Z)-cyano[3-(3-fluoro-4'-methoxybiphenyl-4-yl)-4-oxo-1,3-thiazolidin-2-ylidene]acetate · ligand · chains A
- FMN · Flavin mononucleotide · ligand · chains A
- ORO · Orotic acid · ligand · chains A
- SO4 · Sulfate ion · ion · 10 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 444 | 0.85 | 0.92 | 65 | 52Y, FMN, ORO |
| 2 | 78 | 0.42 | 0.80 | 19 | empty |
| 3 | 104 | 0.41 | 0.77 | 22 | SO4 |
| 4 | 56 | 0.38 | 0.80 | 14 | SO4 |
Compared structures
- 4YLW · Crystal structure of human dihydroorotate dehydrogenase (DHODH) with No.33 compound · the same entry in another collection · chain A 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 Q02127
- Elsewhere: RCSB PDB 4YLW · PDBe 4YLW · UniProt Q02127
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