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Pyrrolopyrimidine inhibitors of DNA gyrase B and topoisomerase IV, part I: structure guided discovery and optimization of dual targeting agents with potent, broad-spectrum enzymatic activity.
Analyse Pyrrolopyrimidine inhibitors of DNA gyrase B and topoisomerase IV, part I… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4HYM
- Type
- protein
- Length
- 587 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Topoisomerase IV, subunit B
- EC
- 5.99.1.3
- UniProt
- Q2A1P5
- Ligands
- CJC
- Pockets
- 5 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Topoisomerase IV, subunit B (EC 5.99.1.3) | protein | 361 | 33% helix, 31% strand | Q2A1P5 |
| B | Topoisomerase IV, subunit B (EC 5.99.1.3) | protein | 226 | 26% helix, 31% strand | Q2A1P5 |
Ligands and binding sites
- CJC · 7-({4-[(3R)-3-aminopyrrolidin-1-yl]-5-chloro-6-ethyl-7H-pyrrolo[2,3-d]pyrimidin-2-yl}sulfanyl)pyrido[2,3-b]pyrazin-2(1H)-one · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 889 | 0.67 | 0.74 | 77 | empty |
| 2 | 518 | 0.65 | 0.77 | 51 | CJC |
| 3 | 60 | 0.38 | 0.80 | 18 | empty |
| 4 | 97 | 0.38 | 0.76 | 21 | empty |
| 5 | 73 | 0.34 | 0.76 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 322 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 4HYM · Pyrrolopyrimidine inhibitors of dna gyrase b and topoisomerase iv, part i: structure… · 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 Q2A1P5
- Elsewhere: RCSB PDB 4HYM · PDBe 4HYM · UniProt Q2A1P5
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