MolNFT v1 · #150026 · protein
Human PARP1 (ARTD1) - catalytic domain in complex with inhibitor ME0527
6GHK · Poly [ADP-ribose] polymerase 1: “Human PARP1 (ARTD1) - catalytic domain in complex with inhibitor ME0527”. X-ray diffraction, 2 ligands (EZ2, SO4), 5 pockets (best druggability 0.81). MolNFT v1 #150026 on GenesisL1: 3D structure…
- PDB
- 6GHK
- Type
- protein
- Length
- 705 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Poly [ADP-ribose] polymerase 1
- EC
- 2.4.2.30
- UniProt
- P09874
- Ligands
- EZ2, SO4
- Pockets
- 5 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Poly [ADP-ribose] polymerase 1 (EC 2.4.2.30) | protein | 350 | 38% helix, 24% strand | P09874 |
| B | Poly [ADP-ribose] polymerase 1 (EC 2.4.2.30) | protein | 355 | 38% helix, 24% strand | P09874 |
Ligands and binding sites
- EZ2 · ~{N}-[(1~{R})-1-(4-imidazol-1-ylphenyl)ethyl]-3-(4-oxidanylidene-1~{H}-quinazolin-2-yl)propanamide · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1168 | 0.81 | 0.83 | 104 | SO4, EZ2 |
| 2 | 424 | 0.77 | 0.86 | 35 | EZ2 |
| 3 | 102 | 0.48 | 0.81 | 17 | empty |
| 4 | 96 | 0.45 | 0.79 | 16 | empty |
| 5 | 65 | 0.40 | 0.80 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 553 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 6GHK · Human PARP1 (ARTD1) - Catalytic domain in complex with inhibitor ME0527 · 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 P09874
- Elsewhere: RCSB PDB 6GHK · PDBe 6GHK · UniProt P09874
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