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
- 3UXM
- Type
- protein
- Length
- 804 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thymidylate kinase
- EC
- 2.7.4.9
- UniProt
- Q9HZN8
- Ligands
- 0DN, MG
- Pockets
- 7 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 59% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thymidylate kinase (EC 2.7.4.9) | protein | 197 | 58% helix, 14% strand | Q9HZN8 |
| B | Thymidylate kinase (EC 2.7.4.9) | protein | 204 | 61% helix, 13% strand | Q9HZN8 |
| C | Thymidylate kinase (EC 2.7.4.9) | protein | 200 | 58% helix, 14% strand | Q9HZN8 |
| D | Thymidylate kinase (EC 2.7.4.9) | protein | 203 | 59% helix, 13% strand | Q9HZN8 |
Ligands and binding sites
- 0DN · 5'-deoxy-5'-fluorothymidine · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 840 | 0.76 | 0.80 | 58 | MG, 0DN |
| 2 | 224 | 0.73 | 0.88 | 39 | 0DN |
| 3 | 239 | 0.73 | 0.87 | 45 | 0DN |
| 4 | 813 | 0.67 | 0.74 | 66 | empty |
| 5 | 262 | 0.62 | 0.80 | 34 | MG, 0DN |
Interfaces
5 interfaces between chains.
- C–D · 1171 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 389 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 388 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 277 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 259 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 3UXM · Structure Guided Development of Novel Thymidine Mimetics targeting Pseudomonas aeruginosa… · the same entry in another collection · chain D against D, TM-score 1.00
- Q9HZN8 · AlphaFold monomer V2.0 prediction for thymidylate kinase (Q9HZN8) · a predicted model of the same protein · chain A 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 3UXM · PDBe 3UXM · UniProt Q9HZN8
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