MolNFT v1 · #153101 · protein
Crystal structure of human dhodh in complex with inhibitor 1289
6J3B · Dihydroorotate dehydrogenase (quinone), mitochondrial: “Crystal structure of human dhodh in complex with inhibitor 1289”. X-ray diffraction, 6 ligands (FMN, ORO, B5O), 5 pockets (best druggability 0.85). MolNFT v1 #153101 on…
- PDB
- 6J3B
- 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, B5O, NA, SO4, CL
- Pockets
- 5 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dihydroorotate dehydrogenase (quinone), mitochondrial (EC 1.3.5.2) | protein | 366 | 46% helix, 16% strand | Q02127 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · chains A
- ORO · Orotic acid · ligand · chains A
- B5O · (6R)-1-[3,5-bis(fluoranyl)-4-[2-fluoranyl-5-(hydroxymethyl)phenyl]phenyl]-6-propan-2-yl-6,7-dihydro-5H-benzotriazol-4-one · ligand · chains A
- NA · Sodium ion · metal · 2 copies · chains A
- SO4 · Sulfate ion · ion · 6 copies · chains A
- CL · Chloride ion · ion · 3 copies · chains A
- ACT · Acetate ion · additive · 6 copies · chains A
- DMS · Dimethyl sulfoxide · additive · 2 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 | 423 | 0.85 | 0.92 | 61 | FMN, ORO, B5O, NA |
| 2 | 89 | 0.55 | 0.85 | 20 | ACT |
| 3 | 109 | 0.43 | 0.78 | 20 | SO4 |
| 4 | 62 | 0.42 | 0.82 | 14 | ACT |
| 5 | 74 | 0.31 | 0.74 | 16 | empty |
Compared structures
- 6J3B · Crystal structure of human DHODH in complex with inhibitor 1289 · 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 6J3B · PDBe 6J3B · UniProt Q02127
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.