Research workbench
Sulfonylpiperidines as novel, antibacterial inhibitors of gram- positive thymidylate kinase (tmk): compound 11
Analyse Sulfonylpiperidines as novel, antibacterial inhibitors of gram- positive… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4HLD
- Type
- protein
- Length
- 394 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thymidylate kinase
- EC
- 2.7.4.9
- UniProt
- Q6GJI9
- Ligands
- 16T
- Pockets
- 2 · best druggability 0.52
Structure
x-ray diffraction · 2 distinct chains · 60% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thymidylate kinase (EC 2.7.4.9) | protein | 196 | 61% helix, 14% strand | Q6GJI9 |
| B | Thymidylate kinase (EC 2.7.4.9) | protein | 198 | 60% helix, 14% strand | Q6GJI9 |
Ligands and binding sites
- 16T · 1-[(3S)-1-{[3-(3-chlorophenoxy)-4-hydroxyphenyl]sulfonyl}piperidin-3-yl]-5-methylpyrimidine-2,4(1H,3H)-dione · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 206 | 0.52 | 0.77 | 24 | 16T |
| 2 | 183 | 0.51 | 0.77 | 24 | 16T |
Interfaces
1 interface between chains.
- A–B · 1052 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 4HLD · Sulfonylpiperidines as Novel, Antibacterial Inhibitors of Gram-Positive Thymidylate… · the same entry in another collection · chain A against A, TM-score 1.00
- Q6GJI9 · AlphaFold monomer V2.0 prediction for thymidylate kinase (Q6GJI9) · a predicted model of the same protein · chain B against A, TM-score 0.95
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 Q6GJI9
- Elsewhere: RCSB PDB 4HLD · PDBe 4HLD · UniProt Q6GJI9
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