MolNFT v1 · #114974 · protein
Crystal structure of human tankyrase-2 in complex with a pyranopyridone inhibitor
5C5Q: “Crystal structure of human tankyrase-2 in complex with a pyranopyridone inhibitor”. X-ray diffraction, 3 ligands (G9W, ZN, SO4), 4 pockets (best druggability 0.82). MolNFT v1 #114974 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5C5Q
- Type
- protein
- Length
- 414 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
- G9W, ZN, SO4
- Pockets
- 4 · 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, 24% strand | Q9H2K2 |
| C | Tankyrase-2 (EC 2.4.2.30) | protein | 46 | 7% helix, 46% 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
- G9W · (3R)-10-methyl-3-(propan-2-yl)-1,3,4,5-tetrahydro-6H-pyrano[4,3-c]isoquinolin-6-one · ligand · 2 copies · chains A, C, B, D
- 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
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 555 | 0.82 | 0.88 | 62 | G9W, SO4 |
| 2 | 272 | 0.65 | 0.82 | 38 | G9W, SO4 |
| 3 | 152 | 0.48 | 0.77 | 19 | empty |
| 4 | 104 | 0.34 | 0.73 | 24 | empty |
Interfaces
5 interfaces between chains.
- B–D · 3064 Ų buried · 60 hydrogen bonds · protein-protein
- A–C · 3008 Ų buried · 62 hydrogen bonds · protein-protein
- A–B · 553 Ų buried · 2 hydrogen bonds · protein-protein
- C–B · 71 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 56 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5C5Q · 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 5C5Q · PDBe 5C5Q · UniProt Q9H2K2
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