Research workbench
Co-crystal structure of tankyrase 1 with compound 4 [(4S)-3-{trans-4- [6-amino-5-(pyrimidin-2-YL)PYRIDIN-3-YL]CYCLOHEXYL}-5,5-dimethyl-4- phenyl-1,3-oxazolidin-2-one]
Analyse Co-crystal structure of tankyrase 1 with compound 4 [(4S)-3-{trans-4… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4N4V
- Type
- protein
- Length
- 413 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tankyrase-1
- EC
- 2.4.2.30
- UniProt
- O95271
- Ligands
- 2GY, ZN
- Pockets
- 5 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 24% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tankyrase-1 (EC 2.4.2.30) | protein | 211 | 23% helix, 28% strand | O95271 |
| B | Tankyrase-1 (EC 2.4.2.30) | protein | 202 | 25% helix, 28% strand | O95271 |
Ligands and binding sites
- 2GY · (4S)-3-{trans-4-[6-amino-5-(pyrimidin-2-yl)pyridin-3-yl]cyclohexyl}-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 | 479 | 0.70 | 0.80 | 55 | empty |
| 2 | 313 | 0.67 | 0.81 | 30 | 2GY |
| 3 | 421 | 0.66 | 0.79 | 44 | 2GY |
| 4 | 154 | 0.46 | 0.76 | 21 | empty |
| 5 | 61 | 0.39 | 0.80 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 443 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 4N4V · Co-crystal structure of tankyrase 1 with compound 4… · the same entry in another collection · chain A against A, TM-score 1.00
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 O95271
- Elsewhere: RCSB PDB 4N4V · PDBe 4N4V · UniProt O95271
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