MolNFT v1 · #122923 · protein
Crystal structure of M2HTDP2-cat in complex with a small molecule inhibitor
5J42 · Tyrosyl-DNA phosphodiesterase 2: “Crystal structure of M2HTDP2-cat in complex with a small molecule inhibitor”. X-ray diffraction, 2 ligands (6FV, MN), 3 pockets (best druggability 0.69). MolNFT v1 #122923 on GenesisL1: 3D…
- PDB
- 5J42
- Type
- protein
- Length
- 497 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tyrosyl-DNA phosphodiesterase 2
- EC
- 3.1.4.-
- UniProt
- Q9JJX7
- Ligands
- 6FV, MN
- Pockets
- 3 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 23% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tyrosyl-DNA phosphodiesterase 2 (EC 3.1.4.-) | protein | 248 | 23% helix, 37% strand | Q9JJX7 |
| B | Tyrosyl-DNA phosphodiesterase 2 (EC 3.1.4.-) | protein | 249 | 24% helix, 36% strand | Q9JJX7 |
Ligands and binding sites
- 6FV · 10-(4-hydroxyphenyl)-2,4-dioxo-2,3,4,10-tetrahydropyrimido[4,5-b]quinoline-8-carbonitrile · ligand · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
- TLA · L(+)-tartaric acid · additive · 6 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 657 | 0.69 | 0.77 | 57 | 6FV, TLA, MN |
| 2 | 81 | 0.43 | 0.80 | 18 | empty |
| 3 | 60 | 0.27 | 0.73 | 16 | EDO |
Interfaces
1 interface between chains.
- A–B · 461 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5J42 · Crystal structure of m2hTDP2-CAT in complex with a small molecule inhibitor · the same entry in another collection · chain A against A, TM-score 1.00
- Q9JJX7 · AlphaFold monomer V2.0 prediction for tyrosyl-DNA phosphodiesterase 2 (Q9JJX7) · a predicted model of the same protein · chain B 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 Q9JJX7
- Elsewhere: RCSB PDB 5J42 · PDBe 5J42 · UniProt Q9JJX7
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