Research workbench
Crystal structure of human parp-1 cat domain bound to inhibitor UKTT15
Analyse Crystal structure of human parp-1 cat domain bound to inhibitor UKTT15 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VKO
- Type
- protein
- Length
- 1,360 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Poly [ADP-ribose] polymerase 1
- EC
- 2.4.2.30, 2.4.2.-
- UniProt
- P09874
- Ligands
- L1S, SO4
- Pockets
- 14 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Poly [ADP-ribose] polymerase 1 (EC 2.4.2.30, 2.4.2.-) | protein | 340 | 34% helix, 25% strand | P09874 |
Ligands and binding sites
- L1S · Methyl 2-{4-[4-(7-carbamoyl-1H-benzimidazol-2-yl) benzene-1-carbonyl]piperazin-1-yl}pyrimidine-5-carboxylate · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 12 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 593 | 0.79 | 0.85 | 47 | L1S |
| 2 | 600 | 0.78 | 0.84 | 51 | L1S |
| 3 | 606 | 0.78 | 0.84 | 46 | L1S |
| 4 | 595 | 0.78 | 0.84 | 46 | L1S |
| 5 | 715 | 0.72 | 0.78 | 86 | empty |
Interfaces
3 interfaces between chains.
- C–D · 532 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 531 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 524 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 6VKO · Crystal Structure of human PARP-1 CAT domain bound to inhibitor UKTT15 · 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 6VKO · PDBe 6VKO · UniProt P09874
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