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Human thymidylate synthase bound to dump and LY231514, a PYRROLO(2,3- D)PYRIMIDINE-based antifolate
Analyse Human thymidylate synthase bound to dump and LY231514, a PYRROLO(2,3… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1JUJ
- Type
- protein
- Length
- 1,144 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thymidylate synthase
- EC
- 2.1.1.45
- UniProt
- P04818
- Ligands
- UMP, LYA
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Thymidylate synthase (EC 2.1.1.45) | protein | 286 | 34% helix, 21% strand | P04818 |
Ligands and binding sites
- UMP · 2'-deoxyuridine 5'-monophosphate · ligand · 4 copies · chains A, B, C, D
- LYA · 2-{4-[2-(2-amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidin-5-yl)-ethyl]-benzoylamino}-pentanedioic acid · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 374 | 0.77 | 0.87 | 39 | UMP, LYA |
| 2 | 383 | 0.77 | 0.86 | 41 | UMP, LYA |
| 3 | 383 | 0.77 | 0.86 | 38 | UMP, LYA |
| 4 | 369 | 0.76 | 0.87 | 39 | UMP, LYA |
| 5 | 168 | 0.52 | 0.78 | 23 | empty |
Interfaces
4 interfaces between chains.
- A–B · 2166 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 2159 Ų buried · 20 hydrogen bonds · protein-protein
- B–D · 311 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 13 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 1JUJ · Human Thymidylate Synthase Bound to dUMP and LY231514, a Pyrrolo(2,3-d)pyrimidine-based… · the same entry in another collection · chain A against A, TM-score 1.00
- P04818 · AlphaFold monomer V2.0 prediction for thymidylate synthase (P04818) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 1JUJ · PDBe 1JUJ · UniProt P04818
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