MolNFT v1 · #55567 · protein
Plasmodium falciparum thymidylate kinase in complex with a urea-alpha-deoxythymidine inhibitor
2YOH: “Plasmodium falciparum thymidylate kinase in complex with a urea-alpha-deoxythymidine inhibitor”. X-ray diffraction, 1 ligand (WMJ), 3 pockets (best druggability 0.59). MolNFT v1 #55567 on GenesisL1: 3D structure, binding sites and…
- PDB
- 2YOH
- 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
- Q8I4S1
- Ligands
- WMJ
- Pockets
- 3 · best druggability 0.59
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 | 199 | 47% helix, 16% strand | Q8I4S1 |
| B | Thymidylate kinase (EC 2.7.4.9) | protein | 199 | 47% helix, 16% strand | Q8I4S1 |
Ligands and binding sites
- WMJ · 1-[[(2R,3S,5S)-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methyl]-3-(4-nitrophenyl)urea · 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 | 254 | 0.59 | 0.79 | 32 | WMJ |
| 2 | 184 | 0.57 | 0.81 | 27 | WMJ |
| 3 | 63 | 0.28 | 0.73 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 763 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 2YOH · Plasmodium falciparum thymidylate kinase in complex with a urea-alpha- deoxythymidine… · 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 2YOH · PDBe 2YOH · UniProt Q8I4S1
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