MolNFT v1 · #69611 · protein
Crystal structure of human dihydroorotate dehydrogenase (dhodh) with amino-benzoic acid inhibitor 715 at 1.85A resolution
3KVL · Dihydroorotate dehydrogenase, mitochondrial: “Crystal structure of human dihydroorotate dehydrogenase (dhodh) with amino-benzoic acid inhibitor 715 at…”. X-ray diffraction, 5 ligands (FMN, DOR, DET), 5 pockets (best druggability…
- PDB
- 3KVL
- Type
- protein
- Length
- 359 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydroorotate dehydrogenase, mitochondrial
- EC
- 1.3.5.2
- UniProt
- Q02127
- Ligands
- FMN, DOR, DET, 7Z5, SO4
- Pockets
- 5 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dihydroorotate dehydrogenase, mitochondrial (EC 1.3.5.2) | protein | 359 | 45% helix, 16% strand | Q02127 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · chains A
- DOR · (4S)-2,6-dioxohexahydropyrimidine-4-carboxylic acid · ligand · chains A
- DET · Undecylamine-N,N-dimethyl-N-oxide · ligand · chains A
- 7Z5 · 5-[methyl(pyridin-3-ylmethyl)amino]-2-(propanoylamino)benzoic acid · ligand · chains A
- SO4 · Sulfate ion · ion · chains A
- ACT · Acetate ion · additive · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 448 | 0.84 | 0.91 | 63 | FMN, DOR, 7Z5 |
| 2 | 96 | 0.43 | 0.79 | 20 | DET |
| 3 | 89 | 0.41 | 0.78 | 19 | empty |
| 4 | 70 | 0.38 | 0.78 | 15 | empty |
| 5 | 79 | 0.34 | 0.76 | 17 | empty |
Compared structures
- 3KVL · Crystal structure of human dihydroorotate dehydrogenase (DHODH) with amino-benzoic acid… · 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 3KVL · PDBe 3KVL · UniProt Q02127
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