MolNFT v1 · #11677 · protein
E. COLI ts complex with dump and the PYRROLO(2,3-D)PYRIMIDINE-based antifolate LY341770
1JTQ · Thymidylate synthase: “E. COLI ts complex with dump and the PYRROLO(2,3-D)PYRIMIDINE-based antifolate LY341770”. X-ray diffraction, 2 ligands (UMP, LY3), 7 pockets (best druggability 0.76). MolNFT v1 #11677 on GenesisL1: 3D…
- PDB
- 1JTQ
- Type
- protein
- Length
- 528 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thymidylate synthase
- EC
- 2.1.1.45
- UniProt
- P0A884
- Ligands
- UMP, LY3
- Pockets
- 7 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Thymidylate synthase (EC 2.1.1.45) | protein | 264 | 34% helix, 26% strand | P0A884 |
Ligands and binding sites
- UMP · 2'-deoxyuridine 5'-monophosphate · ligand · 2 copies · chains A, B
- LY3 · 2-{4-[2-(2-amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidin-5-yl)-ethyl]-benzoylamino}-4-(2H-tetrazol-5-yl)-butyric acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 548 | 0.76 | 0.83 | 60 | UMP, LY3 |
| 2 | 430 | 0.76 | 0.85 | 43 | UMP, LY3 |
| 3 | 100 | 0.43 | 0.78 | 17 | empty |
| 4 | 98 | 0.41 | 0.78 | 20 | empty |
| 5 | 106 | 0.38 | 0.75 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 2389 Ų buried · 36 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 2 modified (covalent ligand, carboxylation).
Compared structures
- 1JTQ · E. coli TS Complex with dUMP and the Pyrrolo(2,3-d)pyrimidine-based Antifolate LY341770 · the same entry in another collection · chain A against A, TM-score 1.00
- P0A884 · AlphaFold monomer V2.0 prediction for thymidylate synthase (P0A884) · a predicted model of the same protein · 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 P0A884
- Elsewhere: RCSB PDB 1JTQ · PDBe 1JTQ · UniProt P0A884
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