MolNFT v1 · #9422 · protein
Human thymidylate synthase complexed with dump and raltitrexed, an antifolate drug, is in the closed conformation
1HVY: “Human thymidylate synthase complexed with dump and raltitrexed, an antifolate drug, is in the closed…”. X-ray diffraction, 2 ligands (D16, UMP), 14 pockets (best druggability 0.77). MolNFT v1 #9422 on GenesisL1: 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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