MolNFT v1 · #191230 · protein
Cryo-EM structure of mtb lpd bound to inhibitor complex with 2-((2- cyano-N,5-dimethyl-1H-indole)-7-sulfonamido)-N-(4-(oxetan-3-yl)-3,4- dihydro-2H-BENZO[B] [1,4]OXAZIN-7-YL)ACETAMIDE
8CT4 · Dihydrolipoyl dehydrogenase: “Cryo-EM structure of mtb lpd bound to inhibitor complex with 2-((2…”. Electron microscopy, 2 ligands (FAD, OU6), 9 pockets (best druggability 0.82). MolNFT v1 #191230 on GenesisL1: 3D structure, binding…
- PDB
- 8CT4
- Type
- protein
- Length
- 928 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydrolipoyl dehydrogenase
- EC
- 1.8.1.4
- UniProt
- P9WHH9
- Ligands
- FAD, OU6
- Pockets
- 9 · best druggability 0.82
Structure
electron microscopy · 1 distinct chain · 35% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Dihydrolipoyl dehydrogenase (EC 1.8.1.4) | protein | 464 | 35% helix, 27% strand | P9WHH9 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- OU6 · N~2~-(2-cyano-5-methyl-1H-indole-7-sulfonyl)-N~2~-methyl-N-[4-(oxetan-3-yl)-3,4-dihydro-2H-1,4-benzoxazin-7-yl]glycinamide · 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, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 183 | 0.82 | 0.97 | 35 | empty |
| 2 | 1016 | 0.81 | 0.83 | 104 | FAD |
| 3 | 1022 | 0.81 | 0.82 | 99 | FAD |
| 4 | 138 | 0.72 | 0.91 | 27 | OU6 |
| 5 | 146 | 0.71 | 0.90 | 26 | OU6 |
Interfaces
1 interface between chains.
- A–B · 3818 Ų buried · 46 hydrogen bonds · protein-protein
Compared structures
- 8CT4 · Cryo-EM structure of Mtb Lpd bound to inhibitor complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- P9WHH9 · AlphaFold monomer V2.0 prediction for dihydrolipoyl dehydrogenase (P9WHH9) · a predicted model of the same protein · chain B 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 P9WHH9
- Elsewhere: RCSB PDB 8CT4 · PDBe 8CT4 · UniProt P9WHH9
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