MolNFT v1 · #88630 · protein
Mtb inha complex with pyradizinone compound 14
4D0S · Enoyl-[acyl-carrier-protein] reductase [NADH]: “Mtb inha complex with pyradizinone compound 14”. X-ray diffraction, 3 ligands (NAD, 9G4, MG), 11 pockets (best druggability 0.84). MolNFT v1 #88630 on GenesisL1: 3D structure, binding…
- PDB
- 4D0S
- Type
- protein
- Length
- 1,022 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Enoyl-[acyl-carrier-protein] reductase [NADH]
- EC
- 1.3.1.9
- UniProt
- P9WGR0
- Ligands
- NAD, 9G4, MG
- Pockets
- 11 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 44% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Enoyl-[acyl-carrier-protein] reductase [NADH] (EC 1.3.1.9) | protein | 256 | 44% helix, 18% strand | P9WGR0 |
| B | Enoyl-[acyl-carrier-protein] reductase [NADH] (EC 1.3.1.9) | protein | 252 | 44% helix, 18% strand | P9WGR0 |
| C | Enoyl-[acyl-carrier-protein] reductase [NADH] (EC 1.3.1.9) | protein | 255 | 45% helix, 18% strand | P9WGR0 |
| D | Enoyl-[acyl-carrier-protein] reductase [NADH] (EC 1.3.1.9) | protein | 259 | 44% helix, 17% strand | P9WGR0 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
- 9G4 · 1-{4-[(acetylamino)methyl]phenyl}-4-(4-chlorophenoxy)-6-oxo-1,6-dihydropyridazine-3-carboxamide · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 2 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1137 | 0.84 | 0.85 | 55 | empty |
| 2 | 650 | 0.75 | 0.81 | 51 | NAD, 9G4 |
| 3 | 567 | 0.72 | 0.80 | 50 | NAD, 9G4 |
| 4 | 546 | 0.72 | 0.80 | 49 | NAD, 9G4 |
| 5 | 496 | 0.69 | 0.79 | 42 | NAD, 9G4 |
Interfaces
6 interfaces between chains.
- B–D · 1577 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 1576 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 1508 Ų buried · 19 hydrogen bonds · protein-protein
- A–D · 1444 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 642 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
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 P9WGR0
- Elsewhere: RCSB PDB 4D0S · PDBe 4D0S · UniProt P9WGR0
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