Research workbench
Structure guided development of novel thymidine mimetics targeting pseudomonas aeruginosa thymidylate kinase: from hit to lead generation
Analyse Structure guided development of novel thymidine mimetics targeting pseudomonas… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3UWK
- Type
- protein
- Length
- 398 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thymidylate kinase
- EC
- 2.7.4.9
- UniProt
- Q9HZN8
- Ligands
- 0DF, MG
- Pockets
- 3 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 58% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thymidylate kinase (EC 2.7.4.9) | protein | 202 | 60% helix, 13% strand | Q9HZN8 |
| B | Thymidylate kinase (EC 2.7.4.9) | protein | 196 | 55% helix, 14% strand | Q9HZN8 |
Ligands and binding sites
- 0DF · 1-methyl-6-phenyl-1,3-dihydro-2H-imidazo[4,5-b]pyridin-2-one · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 186 | 0.74 | 0.91 | 37 | 0DF |
| 2 | 130 | 0.65 | 0.88 | 25 | 0DF |
| 3 | 643 | 0.63 | 0.74 | 60 | empty |
Interfaces
1 interface between chains.
- A–B · 256 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 3UWK · Structure Guided Development of Novel Thymidine Mimetics targeting Pseudomonas aeruginosa… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9HZN8 · AlphaFold monomer V2.0 prediction for thymidylate kinase (Q9HZN8) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 Q9HZN8
- Elsewhere: RCSB PDB 3UWK · PDBe 3UWK · UniProt Q9HZN8
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