MolNFT v1 · #59108 · protein
Crystal structure of thymidylate synthase ternary complex with dump and 8A inhibitor
3BNZ: “Crystal structure of thymidylate synthase ternary complex with dump and 8A inhibitor”. X-ray diffraction, 3 ligands (UMP, C16, PO4), 2 pockets (best druggability 0.73). MolNFT v1 #59108 on GenesisL1: 3D structure, binding sites and…
- 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
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