MolNFT v1 · #87227 · protein + DNA
Novel hydroxyl tricyclics (E.G. GSK966587) as potent inhibitors of bacterial type iia topoisomerases
4BUL · DNA gyrase subunit B, DNA gyrase subunit a: “Novel hydroxyl tricyclics (E.G. GSK966587) as potent inhibitors of bacterial type iia topoisomerases”. X-ray diffraction, 2 ligands (AE8, MN), 17 pockets (best druggability 0.84). MolNFT…
- PDB
- 4BUL
- Type
- protein + DNA
- Length
- 1,423 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA gyrase subunit B, DNA gyrase subunit a; 5'-D(*TP*GP*TP*GP*CP*GP*GP*TP*GP*TP*AP*CP*CP*T…
- EC
- 5.99.1.3
- UniProt
- P66937, Q99XG5
- Ligands
- AE8, MN
- Pockets
- 17 · best druggability 0.84
Structure
x-ray diffraction · 6 distinct chains · 48% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA gyrase subunit B, DNA gyrase subunit a (EC 5.99.1.3) | protein | 674 | 47% helix, 16% strand | P66937, Q99XG5 |
| C | DNA gyrase subunit B, DNA gyrase subunit a (EC 5.99.1.3) | protein | 671 | 48% helix, 16% strand | P66937, Q99XG5 |
| E | 5'-D(*TP*GP*TP*GP*CP*GP*GP*TP*GP*TP*AP*CP*CP*TP *AP*CP*GP*GP*CP*T)-3' | dna | 20 | — | — |
| F | 5'-D(*AP*GP*CP*CP*GP*TP*AP*GP*GP*TP*AP*CP*AP*CP *CP*GP*CP*AP*C)-3' | dna | 19 | — | — |
| G | 5'-D(*TP*GP*TP*GP*CP*GP*GP*TP*GP*TP*AP*CP*CP*TP *AP*CP*GP*GP*CP*T)-3' | dna | 19 | — | — |
| H | 5'-D(*AP*GP*CP*CP*GP*TP*AP*GP*GP*TP*AP*CP*AP*CP *CP*GP*CP*AP*C)-3' | dna | 20 | — | — |
Ligands and binding sites
- AE8 · (S)-4-((4-(((2,3-dihydro-[1,4]dioxino[2,3-c]pyridin-7-yl)methyl)amino)piperidin-1-yl)methyl)-3-fluoro-4-hydroxy-4H-pyrrolo[3,2,1-de][1,5]naphthyridin-7(5H)-one · ligand · chains A, C, E, F, G, H
- MN · Manganese (II) ion · metal · 4 copies · chains A, E, H, C, F, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1031 | 0.84 | 0.85 | 129 | AE8 |
| 2 | 458 | 0.74 | 0.84 | 42 | empty |
| 3 | 392 | 0.69 | 0.82 | 39 | empty |
| 4 | 520 | 0.64 | 0.76 | 51 | empty |
| 5 | 383 | 0.64 | 0.79 | 48 | empty |
Interfaces
15 interfaces between chains.
- A–C · 3178 Ų buried · 43 hydrogen bonds · protein-protein
- E–H · 2336 Ų buried · 797 hydrogen bonds · nucleic-nucleic
- F–G · 2237 Ų buried · 759 hydrogen bonds · nucleic-nucleic
- A–H · 994 Ų buried · 20 hydrogen bonds · protein-nucleic
- A–E · 992 Ų buried · 21 hydrogen bonds · protein-nucleic
Compared structures
- 4BUL · Novel hydroxyl tricyclics (e.g. GSK966587) as potent inhibitors of bacterial type IIA… · the same entry in another collection · chain H against H, TM-score 1.00
- Q99XG5 · AlphaFold monomer V2.0 prediction for DNA gyrase subunit a (Q99XG5) · a predicted model of the same protein · chain A against A, TM-score 0.71
- P66937 · AlphaFold monomer V2.0 prediction for DNA gyrase subunit B (P66937) · a predicted model of the same protein · chain A against A, TM-score 0.28
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 P66937
- Every structure of UniProt Q99XG5
- Elsewhere: RCSB PDB 4BUL · PDBe 4BUL · UniProt P66937 · UniProt Q99XG5
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