MolNFT v1 · #151993 · protein
Plasmodium falciparum dihydroorotate dehydrogenase (dhodh) co- crystallized with 3-hydroxy-1-methyl-5-((3-(TRIFLUOROMETHYL)PHENOXY) methyl)-1H-pyrazole-4-carboxylic acid
6I4B: “Plasmodium falciparum dihydroorotate dehydrogenase (dhodh) co- crystallized with…”. X-ray diffraction, 3 ligands (FMN, ORO, E2N), 7 pockets (best druggability 0.84). MolNFT v1 #151993 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6I4B
- Type
- protein
- Length
- 755 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydroorotate dehydrogenase
- UniProt
- Q54A96
- Ligands
- FMN, ORO, E2N
- Pockets
- 7 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dihydroorotate dehydrogenase | protein | 381 | 44% helix, 16% strand | Q54A96 |
| B | Dihydroorotate dehydrogenase | protein | 374 | 44% helix, 17% strand | Q54A96 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 2 copies · chains A, B
- ORO · Orotic acid · ligand · 2 copies · chains A, B
- E2N · 1-methyl-3-oxidanyl-5-[[3-(trifluoromethyl) phenoxy]methyl]pyrazole-4-carboxylic acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 369 | 0.84 | 0.93 | 56 | FMN, ORO, E2N |
| 2 | 863 | 0.82 | 0.84 | 97 | FMN, ORO, E2N |
| 3 | 334 | 0.55 | 0.75 | 24 | empty |
| 4 | 102 | 0.42 | 0.77 | 20 | empty |
| 5 | 88 | 0.41 | 0.78 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 507 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6I4B · Plasmodium falciparum dihydroorotate dehydrogenase (DHODH) co-crystallized with… · 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 Q54A96
- Elsewhere: RCSB PDB 6I4B · PDBe 6I4B · UniProt Q54A96
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