MolNFT v1 · #168123 · protein
Human PARP16 in complex with RBN010860
6W65 · Protein mono-ADP-ribosyltransferase PARP16: “Human PARP16 in complex with RBN010860”. X-ray diffraction, 1 ligand (T9D), 11 pockets (best druggability 0.76). MolNFT v1 #168123 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6W65
- Type
- protein
- Length
- 714 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein mono-ADP-ribosyltransferase PARP16
- EC
- 2.4.2.-
- UniProt
- Q8N5Y8
- Ligands
- T9D
- Pockets
- 11 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein mono-ADP-ribosyltransferase PARP16 (EC 2.4.2.-) | protein | 243 | 40% helix, 23% strand | Q8N5Y8 |
| B | Protein mono-ADP-ribosyltransferase PARP16 (EC 2.4.2.-) | protein | 234 | 41% helix, 24% strand | Q8N5Y8 |
| C | Protein mono-ADP-ribosyltransferase PARP16 (EC 2.4.2.-) | protein | 237 | 41% helix, 24% strand | Q8N5Y8 |
Ligands and binding sites
- T9D · 5-{5-[(piperidin-4-yl)oxy]-2H-isoindol-2-yl}-4-(trifluoromethyl)pyridazin-3(2H)-one · ligand · 3 copies · chains A, B, C
- GOL · Glycerol · additive · 10 copies · chains A, C, B
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B, C
- CIT · Citric acid · additive · 2 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains B, A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 793 | 0.76 | 0.80 | 79 | GOL, PEG |
| 2 | 311 | 0.59 | 0.77 | 37 | T9D, CIT |
| 3 | 137 | 0.51 | 0.80 | 20 | empty |
| 4 | 140 | 0.51 | 0.79 | 18 | empty |
| 5 | 211 | 0.48 | 0.75 | 24 | empty |
Interfaces
2 interfaces between chains.
- A–B · 856 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 599 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
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 Q8N5Y8
- Elsewhere: RCSB PDB 6W65 · PDBe 6W65 · UniProt Q8N5Y8
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.