MolNFT v1 · #139139 · protein
Human thymidylate synthase in complex with dump and nolatrexed
5X67: “Human thymidylate synthase in complex with dump and nolatrexed”. X-ray diffraction, 2 ligands (UMP, 7Z9), 5 pockets (best druggability 0.79). MolNFT v1 #139139 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5X67
- Type
- protein
- Length
- 574 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thymidylate synthase
- EC
- 2.1.1.45
- UniProt
- P04818
- Ligands
- UMP, 7Z9
- Pockets
- 5 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thymidylate synthase (EC 2.1.1.45) | protein | 286 | 34% helix, 23% strand | P04818 |
| B | Thymidylate synthase (EC 2.1.1.45) | protein | 288 | 34% helix, 23% strand | P04818 |
Ligands and binding sites
- UMP · 2'-deoxyuridine 5'-monophosphate · ligand · 2 copies · chains A, B
- 7Z9 · 2-azanyl-6-methyl-5-pyridin-4-ylsulfanyl-3H-quinazolin-4-one · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 549 | 0.79 | 0.85 | 60 | UMP, 7Z9 |
| 2 | 369 | 0.79 | 0.88 | 44 | UMP, 7Z9 |
| 3 | 181 | 0.51 | 0.77 | 22 | empty |
| 4 | 160 | 0.43 | 0.74 | 25 | empty |
| 5 | 60 | 0.35 | 0.78 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 2220 Ų buried · 35 hydrogen bonds · protein-protein
Compared structures
- 5X67 · Human thymidylate synthase in complex with dUMP and nolatrexed · 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 P04818
- Elsewhere: RCSB PDB 5X67 · PDBe 5X67 · UniProt P04818
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