Research workbench
Optimisation of pyrroleamides as mycobacterial gyrb ATPase inhibitors: structure activity relationship and in vivo efficacy in the mouse model of tuberculosis
Analyse Optimisation of pyrroleamides as mycobacterial gyrb ATPase inhibitors… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4BAE
- Type
- protein
- Length
- 736 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA gyrase subunit B
- EC
- 5.99.1.3
- UniProt
- P0C559
- Ligands
- RWX, CA, SO4
- Pockets
- 12 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 30% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | DNA gyrase subunit B (EC 5.99.1.3) | protein | 184 | 30% helix, 32% strand | P0C559 |
| B | DNA gyrase subunit B (EC 5.99.1.3) | protein | 183 | 31% helix, 32% strand | P0C559 |
| D | DNA gyrase subunit B (EC 5.99.1.3) | protein | 185 | 30% helix, 31% strand | P0C559 |
Ligands and binding sites
- RWX · 2-[(3S,4R)-4-[(3-bromanyl-4-chloranyl-5-methyl-1H-pyrrol-2-yl)carbonylamino]-3-methoxy-piperidin-1-yl]-4-(2-methyl-1,2,4-triazol-3-yl)-1,3-thiazole-5-carboxylic acid · ligand · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · 4 copies · chains A, C, D
- SO4 · Sulfate ion · ion · 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 | 123 | 0.80 | 0.98 | 20 | empty |
| 2 | 117 | 0.79 | 0.98 | 20 | empty |
| 3 | 163 | 0.56 | 0.81 | 22 | RWX |
| 4 | 171 | 0.55 | 0.80 | 26 | RWX |
| 5 | 171 | 0.54 | 0.79 | 23 | RWX |
Interfaces
2 interfaces between chains.
- C–D · 932 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 900 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 4BAE · Optimisation of pyrroleamides as mycobacterial GyrB ATPase inhibitors: Structure Activity… · the same entry in another collection · chain A against A, TM-score 1.00
- P0C559 · AlphaFold monomer V2.0 prediction for DNA gyrase subunit B (P0C559) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 P0C559
- Elsewhere: RCSB PDB 4BAE · PDBe 4BAE · UniProt P0C559
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