MolNFT v1 · #40696 · protein
Structural basis for non-competitive product inhibition in human thymidine phosphorylase: implication for drug design
2J0F: “Structural basis for non-competitive product inhibition in human thymidine phosphorylase: implication for…”. X-ray diffraction, 1 ligand (TDR), 20 pockets (best druggability 0.78). MolNFT v1 #40696 on GenesisL1: 3D structure…
- PDB
- 2J0F
- Type
- protein
- Length
- 1,784 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thymidine phosphorylase
- EC
- 2.4.2.4
- UniProt
- P19971
- Ligands
- TDR
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Thymidine phosphorylase (EC 2.4.2.4) | protein | 446 | 47% helix, 16% strand | P19971 |
Ligands and binding sites
- TDR · Thymine · ligand · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 725 | 0.78 | 0.82 | 90 | TDR |
| 2 | 113 | 0.77 | 0.97 | 26 | TDR |
| 3 | 115 | 0.77 | 0.96 | 33 | empty |
| 4 | 413 | 0.75 | 0.85 | 51 | TDR |
| 5 | 51 | 0.68 | 0.98 | 24 | empty |
Interfaces
4 interfaces between chains.
- A–C · 1238 Ų buried · 25 hydrogen bonds · protein-protein
- B–D · 1234 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 555 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 196 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 2J0F · Structural basis for non-competitive product inhibition in human thymidine phosphorylase… · the same entry in another collection · chain A against A, TM-score 1.00
- P19971 · AlphaFold monomer V2.0 prediction for thymidine phosphorylase (P19971) · 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 P19971
- Elsewhere: RCSB PDB 2J0F · PDBe 2J0F · UniProt P19971
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