Research workbench
Discovery of selective and potent inhibitors of gram-positive bacterial thymidylate kinase (tmk): compund 16
Analyse Discovery of selective and potent inhibitors of gram-positive bacterial… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4HEJ
- Type
- protein
- Length
- 395 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thymidylate kinase
- EC
- 2.7.4.9
- UniProt
- P65249
- Ligands
- 14D
- Pockets
- 3 · best druggability 0.56
Structure
x-ray diffraction · 2 distinct chains · 59% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thymidylate kinase (EC 2.7.4.9) | protein | 198 | 59% helix, 14% strand | P65249 |
| B | Thymidylate kinase (EC 2.7.4.9) | protein | 197 | 59% helix, 13% strand | P65249 |
Ligands and binding sites
- 14D · 5-methyl-1-[(3S)-1-{3-[3-(trifluoromethyl)phenoxy]benzyl}piperidin-3-yl]pyrimidine-2,4(1H,3H)-dione · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 273 | 0.56 | 0.77 | 36 | 14D |
| 2 | 201 | 0.54 | 0.78 | 34 | empty |
| 3 | 53 | 0.30 | 0.75 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 1040 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 4HEJ · Discovery of Selective and Potent Inhibitors of Gram-positive Bacterial Thymidylate… · the same entry in another collection · chain A against A, TM-score 1.00
- P65249 · AlphaFold monomer V2.0 prediction for thymidylate kinase (P65249) · a predicted model of the same protein · chain A against A, TM-score 0.94
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 P65249
- Elsewhere: RCSB PDB 4HEJ · PDBe 4HEJ · UniProt P65249
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