Research workbench
Dhodh in complex with ligand 13
Analyse Dhodh in complex with ligand 13 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7K2U
- Type
- protein
- Length
- 366 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, VU7, SO4
- Pockets
- 3 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dihydroorotate dehydrogenase (quinone), mitochondrial (EC 1.3.5.2) | protein | 366 | 46% helix, 17% strand | Q02127 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · chains A
- ORO · Orotic acid · ligand · chains A
- VU7 · 6-fluoro-2-(2'-fluoro[1,1'-biphenyl]-4-yl)-N-methoxy-3-methylquinoline-4-carboxamide · ligand · chains A
- SO4 · Sulfate ion · ion · 4 copies · chains A
- ACT · Acetate ion · additive · 4 copies · chains A
- GOL · Glycerol · additive · 2 copies · chains A
- PGE · Triethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 424 | 0.85 | 0.92 | 63 | FMN, ORO, VU7, PGE |
| 2 | 89 | 0.43 | 0.79 | 19 | ACT, GOL |
| 3 | 94 | 0.43 | 0.79 | 18 | GOL, SO4 |
Compared structures
- 7K2U · Dhodh in complex with ligand 13 · 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 7K2U · PDBe 7K2U · UniProt Q02127
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