MolNFT v1 · #155978 · protein
Crystal structure of human dhodh in complex with inhibitor 1243
6LP8 · Dihydroorotate dehydrogenase (quinone), mitochondrial: “Crystal structure of human dhodh in complex with inhibitor 1243”. X-ray diffraction, 5 ligands (FMN, ORO, B6O), 5 pockets (best druggability 0.85). MolNFT v1 #155978 on…
- PDB
- 6LP8
- Type
- protein
- Length
- 365 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, B6O, NA, SO4
- Pockets
- 5 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dihydroorotate dehydrogenase (quinone), mitochondrial (EC 1.3.5.2) | protein | 365 | 47% helix, 16% strand | Q02127 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · chains A
- ORO · Orotic acid · ligand · chains A
- B6O · 3-[4-[3-(dimethylamino)phenyl]-3,5-bis(fluoranyl) phenyl]benzo[f]benzotriazole-4,9-dione · ligand · chains A
- NA · Sodium ion · metal · 3 copies · chains A
- SO4 · Sulfate ion · ion · 2 copies · chains A
- ACT · Acetate ion · additive · 5 copies · chains A
- LDA · Lauryl dimethylamine-N-oxide · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 372 | 0.85 | 0.93 | 63 | FMN, ORO, B6O |
| 2 | 85 | 0.55 | 0.85 | 16 | empty |
| 3 | 116 | 0.46 | 0.79 | 21 | empty |
| 4 | 72 | 0.39 | 0.79 | 19 | ACT, NA |
| 5 | 71 | 0.32 | 0.75 | 17 | empty |
Compared structures
- 6LP8 · Crystal structure of human DHODH in complex with inhibitor 1243 · 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 6LP8 · PDBe 6LP8 · UniProt Q02127
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