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Crystal structure of human DHODH in complex with inhibitor 1289
Analyse Crystal structure of human DHODH in complex with inhibitor 1289 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6J3B
- Type
- protein
- Length
- 366 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.6
- Source
- Homo sapiens
- 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 · resolution 1.6 · 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
- 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 6J3B · PDBe 6J3B · UniProt Q02127
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