Research workbench
Crystal structure of TNKS2 in complex with 2-(2,4- dichlorophenyl)-1-methyl-1H,2H,3H,4H-PYRIDO(2,3-D) pyrimidin-4-one
Analyse Crystal structure of TNKS2 in complex with 2-(2,4… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5AL3
- Type
- protein
- Length
- 417 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tankyrase 2
- EC
- 2.4.2.30
- UniProt
- Q9H2K2
- Ligands
- TGW, ZN, SO4
- Pockets
- 4 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 24% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tankyrase 2 (EC 2.4.2.30) | protein | 208 | 24% helix, 30% strand | Q9H2K2 |
| B | Tankyrase 2 (EC 2.4.2.30) | protein | 209 | 24% helix, 30% strand | Q9H2K2 |
Ligands and binding sites
- TGW · (2R)-2-(2,4-dichlorophenyl)-1-methyl-2,3-dihydropyrido[2,3-d]pyrimidin-4-one · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
- GOL · Glycerol · additive · 4 copies · chains A, B
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 | 458 | 0.81 | 0.88 | 61 | SO4, TGW |
| 2 | 257 | 0.66 | 0.83 | 40 | SO4, TGW |
| 3 | 139 | 0.52 | 0.80 | 18 | empty |
| 4 | 98 | 0.36 | 0.74 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 606 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5AL3 · Crystal structure of TNKS2 in complex with 2-(2,4-dichlorophenyl)-1… · 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 5AL3 · PDBe 5AL3 · UniProt Q9H2K2
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