Research workbench
Crystal structure of human tankyrase-2 in complex with a pyranopyridone inhibitor
Analyse Crystal structure of human tankyrase-2 in complex with a pyranopyridone… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5C5R
- Type
- protein
- Length
- 416 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tankyrase-2
- EC
- 2.4.2.30
- UniProt
- Q9H2K2
- Ligands
- 0E1, ZN, SO4
- Pockets
- 3 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 24% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tankyrase-2 (EC 2.4.2.30) | protein | 161 | 29% helix, 25% strand | Q9H2K2 |
| C | Tankyrase-2 (EC 2.4.2.30) | protein | 48 | 6% helix, 44% strand | Q9H2K2 |
| B | Tankyrase-2 (EC 2.4.2.30) | protein | 160 | 29% helix, 25% strand | Q9H2K2 |
| D | Tankyrase-2 (EC 2.4.2.30) | protein | 47 | 6% helix, 43% strand | Q9H2K2 |
Ligands and binding sites
- 0E1 · (7R)-2-hydroxy-7-(propan-2-yl)-7,8-dihydro-5H-pyrano[4,3-b]pyridine-3-carbonitrile · ligand · 2 copies · chains A, C, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 677 | 0.82 | 0.86 | 76 | 0E1, SO4 |
| 2 | 296 | 0.65 | 0.81 | 42 | 0E1, SO4 |
| 3 | 116 | 0.37 | 0.73 | 24 | empty |
Interfaces
5 interfaces between chains.
- B–D · 3056 Ų buried · 62 hydrogen bonds · protein-protein
- A–C · 3048 Ų buried · 59 hydrogen bonds · protein-protein
- A–B · 549 Ų buried · 3 hydrogen bonds · protein-protein
- C–B · 78 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 52 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5C5R · Crystal structure of human tankyrase-2 in complex with a pyranopyridone inhibitor · 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 Q9H2K2
- Elsewhere: RCSB PDB 5C5R · PDBe 5C5R · UniProt Q9H2K2
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