MolNFT v1 · #146504 · protein
Crystal structure of TDP1 catalytic domain in complex with compound XZ522
6DJI · Tyrosyl-DNA phosphodiesterase 1: “Crystal structure of TDP1 catalytic domain in complex with compound XZ522”. X-ray diffraction, 1 ligand (GOG), 7 pockets (best druggability 0.79). MolNFT v1 #146504 on GenesisL1: 3D structure…
- PDB
- 6DJI
- 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
- GOG
- Pockets
- 7 · 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
- GOG · 3-hydroxybenzene-1,2-dicarboxylic acid · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1192 | 0.79 | 0.81 | 124 | EDO |
| 2 | 256 | 0.53 | 0.76 | 30 | GOG |
| 3 | 235 | 0.51 | 0.76 | 32 | GOG |
| 4 | 79 | 0.41 | 0.79 | 16 | empty |
| 5 | 73 | 0.38 | 0.78 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 722 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6DJI · Crystal structure of Tdp1 catalytic domain in complex with compound XZ522 · 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 6DJI · PDBe 6DJI · UniProt Q9NUW8
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