MolNFT v1 · #178084 · protein
PARP15 catalytic domain in complex with niraparib
7F43 · Protein mono-ADP-ribosyltransferase PARP15: “PARP15 catalytic domain in complex with niraparib”. X-ray diffraction, 1 ligand (3JD), 4 pockets (best druggability 0.79). MolNFT v1 #178084 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7F43
- Type
- protein
- Length
- 396 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein mono-ADP-ribosyltransferase PARP15
- EC
- 2.4.2.-
- UniProt
- Q460N3
- Ligands
- 3JD
- Pockets
- 4 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 22% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein mono-ADP-ribosyltransferase PARP15 (EC 2.4.2.-) | protein | 196 | 23% helix, 30% strand | Q460N3 |
| B | Protein mono-ADP-ribosyltransferase PARP15 (EC 2.4.2.-) | protein | 200 | 22% helix, 29% strand | Q460N3 |
Ligands and binding sites
- 3JD · 2-{4-[(3S)-piperidin-3-yl]phenyl}-2H-indazole-7-carboxamide · ligand · chains 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 346 | 0.79 | 0.89 | 36 | empty |
| 2 | 279 | 0.76 | 0.89 | 31 | empty |
| 3 | 447 | 0.69 | 0.80 | 56 | 3JD |
| 4 | 190 | 0.59 | 0.82 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 1050 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 7F43 · PARP15 catalytic domain in complex with Niraparib · the same entry in another collection · chain A against A, TM-score 1.00
- Q460N3 · AlphaFold monomer V2.0 prediction for protein mono-ADP- ribosyltransferase PARP15 (Q460N3) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 Q460N3
- Elsewhere: RCSB PDB 7F43 · PDBe 7F43 · UniProt Q460N3
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