Research workbench
Targeting myeloid differentiation using potent human dihydroorotate dehydrogenase (hdhodh) inhibitors based on 2-HYDROXYPYRAZOLO[1,5- A]PYRIDINE scaffold
Analyse Targeting myeloid differentiation using potent human dihydroorotate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6FMD
- Type
- protein
- Length
- 357 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
- DUH, FMN, ORO, CL
- Pockets
- 5 · best druggability 0.80
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 | 357 | 46% helix, 17% strand | Q02127 |
Ligands and binding sites
- DUH · 2-oxidanyl-~{N}-[2,3,5,6-tetrakis(fluoranyl)-4-phenyl-phenyl]pyrazolo[1,5-a]pyridine-3-carboxamide · ligand · chains A
- FMN · Flavin mononucleotide · ligand · chains A
- ORO · Orotic acid · ligand · chains A
- CL · Chloride ion · ion · 2 copies · chains A
- ACT · Acetate ion · additive · 6 copies · chains A
- PGE · Triethylene glycol · additive · 6 copies · chains A
- GOL · Glycerol · additive · 4 copies · 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 | 570 | 0.80 | 0.86 | 73 | DUH, FMN, ORO |
| 2 | 65 | 0.52 | 0.86 | 19 | empty |
| 3 | 78 | 0.46 | 0.82 | 19 | PGE |
| 4 | 96 | 0.40 | 0.77 | 21 | ACT |
| 5 | 66 | 0.34 | 0.76 | 16 | empty |
Compared structures
- 6FMD · Targeting myeloid differentiation using potent human dihydroorotate dehydrogenase… · 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 6FMD · PDBe 6FMD · UniProt Q02127
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