MolNFT v1 · #105469 · protein
Human ARTD1 (PARP1) - catalytic domain in complex with inhibitor XAV939
4R5W · Poly [ADP-ribose] polymerase 1: “Human ARTD1 (PARP1) - catalytic domain in complex with inhibitor XAV939”. X-ray diffraction, 2 ligands (XAV, SO4), 6 pockets (best druggability 0.78). MolNFT v1 #105469 on GenesisL1: 3D structure…
- PDB
- 4R5W
- Type
- protein
- Length
- 706 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
- XAV, SO4
- Pockets
- 6 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Poly [ADP-ribose] polymerase 1 (EC 2.4.2.30) | protein | 351 | 39% helix, 22% strand | P09874 |
| B | Poly [ADP-ribose] polymerase 1 (EC 2.4.2.30) | protein | 355 | 39% helix, 22% strand | P09874 |
Ligands and binding sites
- XAV · 2-[4-(trifluoromethyl)phenyl]-7,8-dihydro-5H-thiopyrano[4,3-d]pyrimidin-4-ol · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 7 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 316 | 0.78 | 0.89 | 32 | XAV |
| 2 | 310 | 0.76 | 0.88 | 34 | SO4, XAV |
| 3 | 424 | 0.73 | 0.83 | 48 | SO4 |
| 4 | 108 | 0.48 | 0.80 | 16 | empty |
| 5 | 97 | 0.47 | 0.81 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 612 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 4R5W · Human artd1 (parp1) - catalytic domain in complex with inhibitor xav939 · 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 4R5W · PDBe 4R5W · UniProt P09874
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