Research workbench
Co-crystal structure of tankyrase 1 with compound 3 [(4S)-3-{4-[6- amino-5-(pyrimidin-2-YL)PYRIDIN-3-YL]PHENYL}-5,5-dimethyl-4-phenyl-1, 3-oxazolidin-2-one]
Analyse Co-crystal structure of tankyrase 1 with compound 3 [(4S)-3-{4-[6… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4N4T
- Type
- protein
- Length
- 411 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tankyrase-1
- EC
- 2.4.2.30
- UniProt
- Q6PFX9
- Ligands
- 2GV, ZN
- Pockets
- 5 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 24% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tankyrase-1 (EC 2.4.2.30) | protein | 212 | 24% helix, 27% strand | Q6PFX9 |
| B | Tankyrase-1 (EC 2.4.2.30) | protein | 199 | 25% helix, 27% strand | Q6PFX9 |
Ligands and binding sites
- 2GV · (4S)-3-{4-[6-amino-5-(pyrimidin-2-yl)pyridin-3-yl]phenyl}-5,5-dimethyl-4-phenyl-1,3-oxazolidin-2-one · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 360 | 0.70 | 0.83 | 36 | empty |
| 2 | 292 | 0.68 | 0.82 | 30 | 2GV |
| 3 | 290 | 0.63 | 0.80 | 35 | 2GV |
| 4 | 87 | 0.35 | 0.75 | 20 | empty |
| 5 | 89 | 0.33 | 0.73 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 488 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 4N4T · Co-crystal structure of tankyrase 1 with compound 3… · the same entry in another collection · chain A against A, TM-score 1.00
- Q6PFX9 · AlphaFold monomer V2.0 prediction for poly [ADP-ribose] polymerase tankyrase-1 (Q6PFX9) · a predicted model of the same protein · chain B against A, TM-score 0.76
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 Q6PFX9
- Elsewhere: RCSB PDB 4N4T · PDBe 4N4T · UniProt Q6PFX9
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