MolNFT v1 · #77392 · protein
Crystal structure of thymidine kinase from herpes simplex virus type 1 in complex with N-methyl-fhbt
3RDP: “Crystal structure of thymidine kinase from herpes simplex virus type 1 in complex with N-methyl-fhbt”. X-ray diffraction, 2 ligands (NMF, SO4), 11 pockets (best druggability 0.79). MolNFT v1 #77392 on GenesisL1: 3D structure…
- PDB
- 3RDP
- Type
- protein
- Length
- 634 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thymidine kinase
- EC
- 2.7.1.21
- UniProt
- P03176
- Ligands
- NMF, SO4
- Pockets
- 11 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 55% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thymidine kinase (EC 2.7.1.21) | protein | 314 | 56% helix, 12% strand | P03176 |
| B | Thymidine kinase (EC 2.7.1.21) | protein | 320 | 54% helix, 12% strand | P03176 |
Ligands and binding sites
- NMF · 6-[(2R)-2-(fluoromethyl)-3-hydroxy-propyl]-1,5-dimethyl-pyrimidine-2,4-dione · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 416 | 0.79 | 0.87 | 56 | SO4, NMF |
| 2 | 102 | 0.77 | 0.97 | 17 | NMF |
| 3 | 180 | 0.58 | 0.81 | 29 | empty |
| 4 | 142 | 0.52 | 0.80 | 23 | empty |
| 5 | 130 | 0.50 | 0.80 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 1685 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 3RDP · Crystal structure of thymidine kinase from herpes simplex virus type 1 in complex with… · 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 P03176
- Elsewhere: RCSB PDB 3RDP · PDBe 3RDP · UniProt P03176
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.