MolNFT v1 · #132163 · protein
Pandda analysis group deposition -- crystal structure of DCP2 (NUDT20) in complex with Z2895259681
5QP5: “Pandda analysis group deposition -- crystal structure of DCP2 (NUDT20) in complex with Z2895259681”. X-ray diffraction, 1 ligand (LFY), 1 pocket (best druggability 0.56). MolNFT v1 #132163 on GenesisL1: 3D structure, binding sites…
- PDB
- 5QP5
- 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
- LFY
- Pockets
- 1 · best druggability 0.56
Structure
x-ray diffraction · 1 distinct chain · 23% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DCP2 (NUDT20) (EC 3.6.1.62) | protein | 149 | 23% helix, 30% strand | Q8IU60 |
Ligands and binding sites
- LFY · 1-ethyl-N-[(4-fluorophenyl)methyl]-1H-imidazole-4-carboxamide · ligand · chains A
- EDO · 1,2-ethanediol · additive · 2 copies · chains A
- ACT · Acetate ion · additive · 2 copies · chains A
- DMS · Dimethyl sulfoxide · 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 | 196 | 0.56 | 0.79 | 37 | LFY |
Compared structures
- 5QP5 · 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 5QP5 · PDBe 5QP5 · UniProt Q8IU60
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