Research workbench
Structure of TDP1 catalytic domain in complex with inhibitor XZ633P
Analyse Structure of TDP1 catalytic domain in complex with inhibitor XZ633P in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6W4R
- Type
- protein
- Length
- 876 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tyrosyl-DNA phosphodiesterase 1
- EC
- 3.1.4.-
- UniProt
- Q9NUW8
- Ligands
- SZV
- Pockets
- 6 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 27% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Tyrosyl-DNA phosphodiesterase 1 (EC 3.1.4.-) | protein | 438 | 27% helix, 24% strand | Q9NUW8 |
Ligands and binding sites
- SZV · 4-{[2-(2-hydroxyphenyl)imidazo[1,2-a]pyrazin-3-yl]amino}benzene-1,2-dicarboxylic acid · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, B
- MPO · 3[N-morpholino]propane sulfonic acid · additive · chains A
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 | 992 | 0.79 | 0.80 | 95 | EDO |
| 2 | 198 | 0.59 | 0.81 | 38 | empty |
| 3 | 250 | 0.51 | 0.75 | 35 | MPO, SZV |
| 4 | 208 | 0.49 | 0.75 | 36 | SZV |
| 5 | 65 | 0.38 | 0.79 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 727 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 6W4R · Structure of Tdp1 catalytic domain in complex with inhibitor XZ633p · 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 Q9NUW8
- Elsewhere: RCSB PDB 6W4R · PDBe 6W4R · UniProt Q9NUW8
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.