MolNFT v1 · #117578 · protein
Tankyrase 1 with phthalazinone 1
5ECE · Tankyrase-1: “Tankyrase 1 with phthalazinone 1”. X-ray diffraction, 2 ligands (5N2, ZN), 13 pockets (best druggability 0.80). MolNFT v1 #117578 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5ECE
- Type
- protein
- Length
- 812 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tankyrase-1
- EC
- 2.4.2.30
- UniProt
- O95271
- Ligands
- 5N2, ZN
- Pockets
- 13 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 25% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tankyrase-1 (EC 2.4.2.30) | protein | 208 | 24% helix, 27% strand | O95271 |
| B | Tankyrase-1 (EC 2.4.2.30) | protein | 199 | 26% helix, 28% strand | O95271 |
| C | Tankyrase-1 (EC 2.4.2.30) | protein | 203 | 25% helix, 28% strand | O95271 |
| D | Tankyrase-1 (EC 2.4.2.30) | protein | 202 | 25% helix, 28% strand | O95271 |
Ligands and binding sites
- 5N2 · 2-[4-[3-[(4-oxidanylidene-3~{H}-phthalazin-1-yl)methyl]phenyl]carbonylpiperazin-1-yl]pyridine-3-carbonitrile · ligand · 3 copies · chains A, B, C
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 7 copies · chains A, B, C, D
- ACT · Acetate ion · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1000 | 0.80 | 0.81 | 88 | empty |
| 2 | 1037 | 0.77 | 0.79 | 97 | ACT |
| 3 | 500 | 0.68 | 0.79 | 50 | EDO |
| 4 | 673 | 0.68 | 0.76 | 55 | empty |
| 5 | 312 | 0.61 | 0.79 | 30 | 5N2 |
Interfaces
5 interfaces between chains.
- B–D · 652 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 583 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 581 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 552 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 230 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5ECE · Tankyrase 1 with Phthalazi 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 O95271
- Elsewhere: RCSB PDB 5ECE · PDBe 5ECE · UniProt O95271
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