Research workbench
Plasmodium falciparum thymidylate kinase in complex with a (THIO)UREA-alpha-deoxythymidine inhibitor
Analyse Plasmodium falciparum thymidylate kinase in complex with a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2YOG
- Type
- protein
- Length
- 393 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thymidylate kinase
- EC
- 2.7.4.9
- UniProt
- Q8I4S1
- Ligands
- 74X
- Pockets
- 3 · best druggability 0.58
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thymidylate kinase (EC 2.7.4.9) | protein | 197 | 47% helix, 16% strand | Q8I4S1 |
| B | Thymidylate kinase (EC 2.7.4.9) | protein | 196 | 47% helix, 16% strand | Q8I4S1 |
Ligands and binding sites
- 74X · 1-[4-chloranyl-3-(trifluoromethyl)phenyl]-3-[[(2R,3S)-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxol an-2-yl]methyl]thiourea · 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 | 181 | 0.58 | 0.81 | 27 | 74X |
| 2 | 194 | 0.56 | 0.80 | 27 | 74X |
| 3 | 57 | 0.32 | 0.76 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 762 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 2YOG · Plasmodium falciparum thymidylate kinase in complex with a (thio)urea… · the same entry in another collection · chain A against A, TM-score 1.00
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 Q8I4S1
- Elsewhere: RCSB PDB 2YOG · PDBe 2YOG · UniProt Q8I4S1
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