MolNFT v1 · #183371 · protein
Crystal structure of NUDT4 (diphosphoinositol polyphosphate phosphohydrolase 2) in complex with 4-O-bn-1-pcp-INSP4 (AMR2105)
7NNJ: “Crystal structure of NUDT4 (diphosphoinositol polyphosphate phosphohydrolase 2) in complex with…”. X-ray diffraction, 1 ligand (UJN), 2 pockets (best druggability 0.62). MolNFT v1 #183371 on GenesisL1: 3D structure, binding sites…
- PDB
- 7NNJ
- Type
- protein
- Length
- 264 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Diphosphoinositol polyphosphate phosphohydrolase 2
- EC
- 3.6.1.52
- UniProt
- Q9NZJ9
- Ligands
- UJN
- Pockets
- 2 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Diphosphoinositol polyphosphate phosphohydrolase 2 (EC 3.6.1.52) | protein | 131 | 27% helix, 40% strand | Q9NZJ9 |
| B | Diphosphoinositol polyphosphate phosphohydrolase 2 (EC 3.6.1.52) | protein | 133 | 23% helix, 40% strand | Q9NZJ9 |
Ligands and binding sites
- UJN · [oxidanyl-[(2S,3R,5S,6S)-4-phenylmethoxy-2,3,5,6-tetraphosphonooxy-cyclohexyl]oxy-phosphoryl]methylphosphonic acid · ligand · chains B
- FMT · Formic acid · additive · 5 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 444 | 0.62 | 0.76 | 55 | EDO, FMT |
| 2 | 162 | 0.46 | 0.76 | 30 | FMT, UJN |
Interfaces
1 interface between chains.
- A–B · 370 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 7NNJ · Crystal Structure of NUDT4 (Diphosphoinositol polyphosphate phosphohydrolase 2) in… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9NZJ9 · AlphaFold monomer V2.0 prediction for diphosphoinositol polyphosphate phosphohydrolase 2… · a predicted model of the same protein · chain B against A, TM-score 0.97
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 Q9NZJ9
- Elsewhere: RCSB PDB 7NNJ · PDBe 7NNJ · UniProt Q9NZJ9
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