Research workbench
Crystal structure of thymidylate synthase ternary complex with dump and 8A inhibitor
Analyse Crystal structure of thymidylate synthase ternary complex with dump and 8A… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3BNZ
- Type
- protein
- Length
- 312 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thymidylate synthase
- EC
- 2.1.1.45
- UniProt
- P00469
- Ligands
- UMP, C16, PO4
- Pockets
- 2 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thymidylate synthase (EC 2.1.1.45) | protein | 312 | 40% helix, 22% strand | P00469 |
Ligands and binding sites
- UMP · 2'-deoxyuridine 5'-monophosphate · ligand · chains A
- C16 · 4-(4-methyl-1,3-dioxo-1,3-dihydro-2H-isoindol-2-yl)benzonitrile · ligand · chains A
- PO4 · Phosphate ion · ion · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 818 | 0.73 | 0.78 | 69 | UMP, C16 |
| 2 | 56 | 0.26 | 0.73 | 15 | empty |
Compared structures
- 3BNZ · Crystal structure of Thymidylate Synthase ternary complex with dUMP and 8A inhibitor · the same entry in another collection · chain A against A, TM-score 1.00
- P00469 · AlphaFold monomer V2.0 prediction for thymidylate synthase (P00469) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P00469
- Elsewhere: RCSB PDB 3BNZ · PDBe 3BNZ · UniProt P00469
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.