Research workbench
Discovery of pyrimidine isoxazoles inha in complex with compound 23
Analyse Discovery of pyrimidine isoxazoles inha in complex with compound 23 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4UVI
- Type
- protein
- Length
- 1,041 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
- M9TGV3
- Ligands
- NAD, KXU
- Pockets
- 12 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 45% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Enoyl-[acyl-carrier-protein] reductase [NADH] (EC 1.3.1.9) | protein | 261 | 44% helix, 17% strand | M9TGV3 |
| B | Enoyl-[acyl-carrier-protein] reductase [NADH] (EC 1.3.1.9) | protein | 267 | 47% helix, 17% strand | M9TGV3 |
| C | Enoyl-[acyl-carrier-protein] reductase [NADH] (EC 1.3.1.9) | protein | 249 | 43% helix, 18% strand | M9TGV3 |
| D | Enoyl-[acyl-carrier-protein] reductase [NADH] (EC 1.3.1.9) | protein | 264 | 45% helix, 17% strand | M9TGV3 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
- KXU · 5-{[(4,6-dimethylpyrimidin-2-yl)sulfanyl]methyl}-N-[(2-methylpyridin-4-yl)methyl]-1,2-oxazole-3-carboxamide · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1137 | 0.84 | 0.85 | 55 | empty |
| 2 | 550 | 0.78 | 0.84 | 55 | NAD, KXU |
| 3 | 631 | 0.74 | 0.80 | 47 | NAD, KXU |
| 4 | 545 | 0.71 | 0.80 | 48 | NAD, KXU |
| 5 | 427 | 0.69 | 0.80 | 38 | NAD, KXU |
Interfaces
6 interfaces between chains.
- B–D · 1579 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 1567 Ų buried · 20 hydrogen bonds · protein-protein
- A–D · 1503 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 1501 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 722 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 4UVI · Discovery of pyrimidine isoxazoles InhA in complex with compound 23 · 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 M9TGV3
- Elsewhere: RCSB PDB 4UVI · PDBe 4UVI · UniProt M9TGV3
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