MolNFT v1 · #132145 · protein
Pandda analysis group deposition -- crystal structure of DCP2 (NUDT20) in complex with FMOPL000446A
5QON: “Pandda analysis group deposition -- crystal structure of DCP2 (NUDT20) in complex with FMOPL000446A”. X-ray diffraction, 1 ligand (LDS), 1 pocket (best druggability 0.53). MolNFT v1 #132145 on GenesisL1: 3D structure, binding sites…
- PDB
- 5QON
- Type
- protein
- Length
- 149 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DCP2 (NUDT20)
- EC
- 3.6.1.62
- UniProt
- Q8IU60
- Ligands
- LDS
- Pockets
- 1 · best druggability 0.53
Structure
x-ray diffraction · 1 distinct chain · 24% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DCP2 (NUDT20) (EC 3.6.1.62) | protein | 149 | 24% helix, 27% strand | Q8IU60 |
Ligands and binding sites
- LDS · N-(4-ethoxyphenyl)pyrazine-2-carboxamide · ligand · chains A
- ACT · Acetate ion · additive · 2 copies · chains A
- EDO · 1,2-ethanediol · additive · chains A
- DMS · Dimethyl sulfoxide · additive · chains A
- PEG · Di(hydroxyethyl)ether · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 178 | 0.53 | 0.79 | 31 | PEG |
Compared structures
- 5QON · PanDDA analysis group deposition -- Crystal Structure of DCP2 (NUDT20) in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8IU60 · AlphaFold monomer V2.0 prediction for M7GPPPN-mRNA hydrolase (Q8IU60) · a predicted model of the same protein · chain A against A, TM-score 0.90
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 Q8IU60
- Elsewhere: RCSB PDB 5QON · PDBe 5QON · UniProt Q8IU60
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