Research workbench
Human dihydroorotate dehydrogenase complexed with brequinar analog
Analyse Human dihydroorotate dehydrogenase complexed with brequinar analog in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1D3G
- Type
- protein
- Length
- 360 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydroorotate dehydrogenase
- EC
- 1.3.3.1
- UniProt
- Q02127
- Ligands
- BRE, FMN, ORO, DDQ, SO4
- Pockets
- 5 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dihydroorotate dehydrogenase (EC 1.3.3.1) | protein | 360 | 46% helix, 16% strand | Q02127 |
Ligands and binding sites
- BRE · 2-biphenyl-4-yl-6-fluoro-3-methyl-quinoline-4-carboxylic acid · ligand · chains A
- FMN · Flavin mononucleotide · ligand · chains A
- ORO · Orotic acid · ligand · chains A
- DDQ · Decylamine-N,N-dimethyl-N-oxide · 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 | 455 | 0.84 | 0.91 | 66 | BRE, FMN, ORO, DDQ |
| 2 | 101 | 0.45 | 0.79 | 19 | empty |
| 3 | 118 | 0.41 | 0.76 | 21 | empty |
| 4 | 84 | 0.41 | 0.79 | 18 | empty |
| 5 | 82 | 0.34 | 0.75 | 23 | empty |
Compared structures
- 1D3G · Human dihydroorotate dehydrogenase complexed with brequinar analog · 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 1D3G · PDBe 1D3G · UniProt Q02127
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