MolNFT v1 · #67358 · protein
Structure of mycobacterial lipoamide dehydrogenase bound to a triazaspirodimethoxybenzoyl inhibitor
3II4 · Dihydrolipoyl dehydrogenase: “Structure of mycobacterial lipoamide dehydrogenase bound to a triazaspirodimethoxybenzoyl inhibitor”. X-ray diffraction, 2 ligands (FAD, 3II), 9 pockets (best druggability 0.81). MolNFT v1 #67358 on…
- PDB
- 3II4
- Type
- protein
- Length
- 927 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydrolipoyl dehydrogenase
- EC
- 1.8.1.4
- UniProt
- P66004
- Ligands
- FAD, 3II
- Pockets
- 9 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dihydrolipoyl dehydrogenase (EC 1.8.1.4) | protein | 463 | 36% helix, 27% strand | P66004 |
| B | Dihydrolipoyl dehydrogenase (EC 1.8.1.4) | protein | 464 | 35% helix, 27% strand | P66004 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- 3II · N-[2-(2,4-dichlorophenyl)ethyl]-2-{8-[(2,4-dimethoxyphenyl)carbonyl]-4-oxo-1-phenyl-1,3,8-triazaspiro[4.5]dec-3-yl}acetamide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1020 | 0.81 | 0.82 | 94 | FAD, 3II |
| 2 | 1038 | 0.81 | 0.82 | 99 | FAD, 3II |
| 3 | 142 | 0.80 | 0.97 | 38 | empty |
| 4 | 202 | 0.74 | 0.90 | 39 | empty |
| 5 | 161 | 0.68 | 0.88 | 29 | empty |
Interfaces
1 interface between chains.
- A–B · 3752 Ų buried · 58 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 3II4 · Structure of mycobacterial lipoamide dehydrogenase bound to a triazaspirodimethoxybenzoyl… · 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 P66004
- Elsewhere: RCSB PDB 3II4 · PDBe 3II4 · UniProt P66004
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.