MolNFT v1 · #157473 · protein
Crystal structure of TDP1 catalytic domain in complex with compound XZ574
6N0N · Tyrosyl-DNA phosphodiesterase 1: “Crystal structure of TDP1 catalytic domain in complex with compound XZ574”. X-ray diffraction, 1 ligand (KAY), 6 pockets (best druggability 0.78). MolNFT v1 #157473 on GenesisL1: 3D structure…
- PDB
- 6N0N
- Type
- protein
- Length
- 874 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
- KAY
- Pockets
- 6 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 28% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Tyrosyl-DNA phosphodiesterase 1 (EC 3.1.4.-) | protein | 437 | 28% helix, 24% strand | Q9NUW8 |
Ligands and binding sites
- KAY · 4-methylbenzene-1,2-dicarboxylic acid · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, B
- DMS · Dimethyl sulfoxide · additive · 2 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1014 | 0.78 | 0.80 | 93 | DMS, EDO |
| 2 | 227 | 0.58 | 0.80 | 39 | empty |
| 3 | 247 | 0.53 | 0.76 | 37 | KAY |
| 4 | 239 | 0.51 | 0.76 | 37 | KAY |
| 5 | 70 | 0.37 | 0.78 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 670 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6N0N · Crystal structure of Tdp1 catalytic domain in complex with compound XZ574 · 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 6N0N · PDBe 6N0N · UniProt Q9NUW8
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.