Research workbench
Human thymidylate synthase complexed with dump and raltitrexed, an antifolate drug, is in the closed conformation
Analyse Human thymidylate synthase complexed with dump and raltitrexed, an antifolate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1HVY
- Type
- protein
- Length
- 1,152 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
- D16, UMP
- Pockets
- 14 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Thymidylate synthase (EC 2.1.1.45) | protein | 288 | 34% helix, 23% strand | P04818 |
Ligands and binding sites
- D16 · Tomudex · ligand · 4 copies · chains A, B, C, D
- UMP · 2'-deoxyuridine 5'-monophosphate · ligand · 4 copies · chains A, B, C, D
- BME · Beta-mercaptoethanol · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 469 | 0.77 | 0.85 | 54 | D16, UMP |
| 2 | 423 | 0.76 | 0.85 | 49 | D16, UMP |
| 3 | 434 | 0.75 | 0.84 | 47 | D16, UMP |
| 4 | 606 | 0.74 | 0.81 | 63 | BME, D16, UMP |
| 5 | 144 | 0.53 | 0.80 | 20 | BME |
Interfaces
2 interfaces between chains.
- C–D · 2169 Ų buried · 35 hydrogen bonds · protein-protein
- A–B · 2129 Ų buried · 37 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent, 4 modified (covalent ligand, artifact).
Compared structures
- 1HVY · Human thymidylate synthase complexed with dUMP and Raltitrexed, an antifolate drug, is in… · the same entry in another collection · chain D against D, TM-score 1.00
- P04818 · AlphaFold monomer V2.0 prediction for thymidylate synthase (P04818) · a predicted model of the same protein · chain D 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 1HVY · PDBe 1HVY · UniProt P04818
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