Research workbench
Crystal structure of TNKS2 in complex with 2-[4-(piperidin-1-yl) phenyl]-3,4-dihydroquinazolin-4-one
Analyse Crystal structure of TNKS2 in complex with 2-[4-(piperidin-1-yl)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5NVH
- Type
- protein
- Length
- 417 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
- 9B2, ZN, SO4
- Pockets
- 4 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 26% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tankyrase-2 (EC 2.4.2.30) | protein | 161 | 29% helix, 25% strand | Q9H2K2 |
| I, J | Tankyrase-2 (EC 2.4.2.30) | protein | 47 | 6% helix, 45% strand | Q9H2K2 |
| B | Tankyrase-2 (EC 2.4.2.30) | protein | 162 | 29% helix, 25% strand | Q9H2K2 |
Ligands and binding sites
- 9B2 · 2-(4-piperidin-1-ylphenyl)-3~{H}-quinazolin-4-one · ligand · 2 copies · chains A, I, B, J
- ZN · Zinc ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, I, B, J
- GOL · Glycerol · additive · 2 copies · chains I, B
- PEG · Di(hydroxyethyl)ether · additive · chains A, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 426 | 0.80 | 0.88 | 59 | SO4, 9B2 |
| 2 | 242 | 0.62 | 0.81 | 35 | SO4, 9B2 |
| 3 | 139 | 0.52 | 0.80 | 19 | empty |
| 4 | 113 | 0.38 | 0.74 | 20 | empty |
Interfaces
5 interfaces between chains.
- A–I · 3083 Ų buried · 63 hydrogen bonds · protein-protein
- B–J · 3076 Ų buried · 66 hydrogen bonds · protein-protein
- A–B · 586 Ų buried · 3 hydrogen bonds · protein-protein
- A–J · 91 Ų buried · 0 hydrogen bonds · protein-protein
- I–B · 52 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5NVH · Crystal structure of TNKS2 in complex with 2-[4-(piperidin-1-yl)phenyl]-3,4-dihydroquinazo… · 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 5NVH · PDBe 5NVH · UniProt Q9H2K2
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