MolNFT v1 · #16037 · protein
Crystal structure of human thymidylate kinase with fltmp and ADP
1NMX · Similar to thymidylate kinase (dtmp kinase): “Crystal structure of human thymidylate kinase with fltmp and ADP”. X-ray diffraction, 3 ligands (FDM, ADP, MG), 2 pockets (best druggability 0.64). MolNFT v1 #16037 on GenesisL1: 3D…
- PDB
- 1NMX
- Type
- protein
- Length
- 210 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Similar to thymidylate kinase (dtmp kinase)
- EC
- 2.7.4.9
- UniProt
- P23919
- Ligands
- FDM, ADP, MG
- Pockets
- 2 · best druggability 0.64
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Similar to thymidylate kinase (dtmp kinase) (EC 2.7.4.9) | protein | 210 | 48% helix, 14% strand | P23919 |
Ligands and binding sites
- FDM · 3'-fluoro-3'-deoxythymidine monophosphate · ligand · chains A
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- MG · Magnesium ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 225 | 0.64 | 0.83 | 29 | MG, FDM |
| 2 | 71 | 0.54 | 0.86 | 20 | empty |
Compared structures
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 P23919
- Elsewhere: RCSB PDB 1NMX · PDBe 1NMX · UniProt P23919
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