MolNFT v1 · #103671 · protein
Crystal structure of human tankyrase 2 in complex with NU1025.
4PNM · Tankyrase-2: “Crystal structure of human tankyrase 2 in complex with NU1025.”. X-ray diffraction, 2 ligands (NU1, ZN), 10 pockets (best druggability 0.77). MolNFT v1 #103671 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 4PNM
- Type
- protein
- Length
- 815 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
- NU1, ZN
- Pockets
- 10 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 25% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tankyrase-2 (EC 2.4.2.30) | protein | 199 | 25% helix, 25% strand | Q9H2K2 |
| B | Tankyrase-2 (EC 2.4.2.30) | protein | 209 | 24% helix, 26% strand | Q9H2K2 |
| C | Tankyrase-2 (EC 2.4.2.30) | protein | 210 | 26% helix, 27% strand | Q9H2K2 |
| D | Tankyrase-2 (EC 2.4.2.30) | protein | 197 | 24% helix, 27% strand | Q9H2K2 |
Ligands and binding sites
- NU1 · 8-hydroxy-2-methyl-3-hydro-quinazolin-4-one · ligand · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 2 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 719 | 0.77 | 0.82 | 93 | NU1 |
| 2 | 276 | 0.72 | 0.86 | 38 | empty |
| 3 | 538 | 0.68 | 0.78 | 65 | NU1, EDO |
| 4 | 231 | 0.66 | 0.83 | 28 | NU1 |
| 5 | 67 | 0.51 | 0.86 | 23 | empty |
Interfaces
3 interfaces between chains.
- A–C · 976 Ų buried · 22 hydrogen bonds · protein-protein
- B–D · 871 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 548 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 4PNM · Crystal Structure of human Tankyrase 2 in complex with Nu1025. · 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 4PNM · PDBe 4PNM · UniProt Q9H2K2
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