Research workbench
Crystal structure of tankyrase 1 with compound 4
Analyse Crystal structure of tankyrase 1 with compound 4 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4I9I
- Type
- protein
- Length
- 838 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tankyrase-1
- EC
- 2.4.2.30
- UniProt
- O95271
- Ligands
- 1DY, ZN
- Pockets
- 9 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 24% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tankyrase-1 (EC 2.4.2.30) | protein | 212 | 23% helix, 30% strand | O95271 |
| B | Tankyrase-1 (EC 2.4.2.30) | protein | 211 | 23% helix, 28% strand | O95271 |
| C | Tankyrase-1 (EC 2.4.2.30) | protein | 209 | 23% helix, 31% strand | O95271 |
| D | Tankyrase-1 (EC 2.4.2.30) | protein | 206 | 25% helix, 28% strand | O95271 |
Ligands and binding sites
- 1DY · N-(2-methoxyphenyl)-4-{[3-(4-oxo-3,4-dihydroquinazolin-2-yl)propanoyl]amino}benzamide · ligand · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1125 | 0.78 | 0.80 | 85 | empty |
| 2 | 273 | 0.66 | 0.82 | 30 | 1DY |
| 3 | 323 | 0.65 | 0.80 | 37 | 1DY |
| 4 | 260 | 0.63 | 0.81 | 29 | 1DY |
| 5 | 262 | 0.62 | 0.80 | 32 | 1DY |
Interfaces
3 interfaces between chains.
- B–C · 765 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 275 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 196 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 4I9I · Crystal structure of tankyrase 1 with compound 4 · the same entry in another collection · chain D against D, TM-score 1.00
- O95271 · AlphaFold monomer V2.0 prediction for poly [ADP-ribose] polymerase tankyrase-1 (O95271) · a predicted model of the same protein · chain D against A, TM-score 0.90
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 4I9I · PDBe 4I9I · UniProt O95271
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