MolNFT v1 · #127397 · protein
Crystal structure of potent human dihydroorotate dehydrogenase inhibitors based on hydroxylated azole scaffolds
5MVD · Dihydroorotate dehydrogenase (quinone), mitochondrial: “Crystal structure of potent human dihydroorotate dehydrogenase inhibitors based on hydroxylated azole…”. X-ray diffraction, 4 ligands (FMN, ORO, U91), 4 pockets (best…
- PDB
- 5MVD
- Type
- protein
- Length
- 348 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
- FMN, ORO, U91, CL
- Pockets
- 4 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dihydroorotate dehydrogenase (quinone), mitochondrial (EC 1.3.5.2) | protein | 348 | 47% helix, 17% strand | Q02127 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · chains A
- ORO · Orotic acid · ligand · chains A
- U91 · 1,5-dimethyl-3-oxidanyl-~{N}-[2,3,5,6-tetrakis(fluoranyl)-4-phenyl-phenyl]pyrazole-4-carboxamide · ligand · chains A
- CL · Chloride ion · ion · 3 copies · chains A
- ACT · Acetate ion · additive · 2 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 | 458 | 0.83 | 0.90 | 68 | FMN, ORO, U91 |
| 2 | 82 | 0.42 | 0.80 | 19 | ACT |
| 3 | 122 | 0.40 | 0.74 | 21 | empty |
| 4 | 50 | 0.25 | 0.73 | 14 | empty |
Compared structures
- 5MVD · Crystal structure of potent human Dihydroorotate Dehydrogenase inhibitors based on… · 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 5MVD · PDBe 5MVD · UniProt Q02127
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