MolNFT v1 · #122913 · protein
Crystal structure of the catalytic domain of human tyrosyl DNA phosphodiesterase 2 in complex with a small molecule inhibitor
5J3S · Tyrosyl-DNA phosphodiesterase 2: “Crystal structure of the catalytic domain of human tyrosyl DNA phosphodiesterase 2 in complex with a small…”. X-ray diffraction, 1 ligand (6FQ), 2 pockets (best druggability 0.49). MolNFT v1 #122913…
- PDB
- 5J3S
- Type
- protein
- Length
- 236 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tyrosyl-DNA phosphodiesterase 2
- EC
- 3.1.4.-
- UniProt
- O95551
- Ligands
- 6FQ
- Pockets
- 2 · best druggability 0.49
Structure
x-ray diffraction · 1 distinct chain · 20% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tyrosyl-DNA phosphodiesterase 2 (EC 3.1.4.-) | protein | 236 | 20% helix, 34% strand | O95551 |
Ligands and binding sites
- 6FQ · 2,4-dioxo-10-[3-(1H-tetrazol-5-yl)phenyl]-2,3,4,10-tetrahydropyrimido[4,5-b]quinoline-8-carbonitrile · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 62 | 0.49 | 0.85 | 15 | empty |
| 2 | 54 | 0.42 | 0.82 | 16 | empty |
Compared structures
- 5J3S · Crystal structure of the catalytic domain of human tyrosyl DNA phosphodiesterase 2 in… · the same entry in another collection · chain A against A, TM-score 1.00
- O95551 · AlphaFold monomer V2.0 prediction for tyrosyl-DNA phosphodiesterase 2 (O95551) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 O95551
- Elsewhere: RCSB PDB 5J3S · PDBe 5J3S · UniProt O95551
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