MolNFT v1 · #124241 · protein
Crystal structure of human dihydroorotate dehydrogenase with ML390
5K9C · Dihydroorotate dehydrogenase (quinone), mitochondrial: “Crystal structure of human dihydroorotate dehydrogenase with ML390”. X-ray diffraction, 5 ligands (FNR, ORO, MLJ), 5 pockets (best druggability 0.81). MolNFT v1 #124241 on…
- PDB
- 5K9C
- Type
- protein
- Length
- 355 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
- FNR, ORO, MLJ, SO4, CL
- Pockets
- 5 · best druggability 0.81
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 | 355 | 46% helix, 17% strand | Q02127 |
Ligands and binding sites
- FNR · 1-deoxy-1-(7,8-dimethyl-2,4-dioxo-3,4-dihydro-2H-benzo[g]pteridin-1-id-10(5H)-yl)-5-O-phosphonato-D-ribitol · ligand · chains A
- ORO · Orotic acid · ligand · chains A
- MLJ · ~{N}-[3-oxidanylidene-3-[[(1~{R})-1,2,3,4-tetrahydronaphthalen-1-yl]amino]propyl]-4-(trifluoromethyloxy)benzamide · ligand · chains A
- SO4 · Sulfate ion · ion · 2 copies · chains A
- CL · Chloride ion · ion · 2 copies · chains A
- ACT · Acetate ion · additive · 3 copies · chains A
- GOL · Glycerol · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 497 | 0.81 | 0.88 | 62 | FNR, ORO, MLJ |
| 2 | 97 | 0.47 | 0.81 | 19 | empty |
| 3 | 78 | 0.39 | 0.78 | 19 | ACT |
| 4 | 57 | 0.32 | 0.76 | 16 | empty |
| 5 | 74 | 0.31 | 0.73 | 15 | empty |
Compared structures
- 5K9C · Crystal structure of human dihydroorotate dehydrogenase with ML390 · 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 5K9C · PDBe 5K9C · UniProt Q02127
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