Research workbench
Tmk from S.AUREUS in complex with the piperidinyl thymine class inhibitor with a C5 ethyl-amine
Analyse Tmk from S.AUREUS in complex with the piperidinyl thymine class inhibitor with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4XWA
- 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
- A7WYM2
- Ligands
- 43N
- Pockets
- 3 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 59% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thymidylate kinase (EC 2.7.4.9) | protein | 200 | 59% helix, 14% strand | A7WYM2 |
| B | Thymidylate kinase (EC 2.7.4.9) | protein | 198 | 59% helix, 14% strand | A7WYM2 |
Ligands and binding sites
- 43N · 2-(3-chlorophenoxy)-6-(ethylamino)-4-[(R)-[(3S)-3-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)piperidin-1-yl](phenyl)methyl]benzoic acid · ligand · 2 copies · chains A, B
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 | 1023 | 0.76 | 0.79 | 83 | 43N |
| 2 | 193 | 0.51 | 0.77 | 21 | 43N |
| 3 | 55 | 0.33 | 0.77 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 243 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4XWA · TMK from S.aureus in complex with the Piperidinyl Thymine class inhibitor with a C5… · the same entry in another collection · chain A against A, TM-score 1.00
- A7WYM2 · AlphaFold monomer V2.0 prediction for thymidylate kinase (A7WYM2) · 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 A7WYM2
- Elsewhere: RCSB PDB 4XWA · PDBe 4XWA · UniProt A7WYM2
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