3949 tRNA delta(2)-isopentenylpyrophosphate transferase helical insertion domain
Ligands and drugs
Aggregated over all current member domains of this group. Drug annotations come from DrugDomain; buffers and crystallization additives are excluded from the tables below.
Chemical profile
ClassyFire chemical superclasses of the ligands bound by this X-group's proteins, from DrugDomain annotations.
The raw number of superclasses rises with the number of proteins sampled; the per-20 value compares X-groups at equal depth.
| Superclass | Proteins | Expected | 0.25×observed / expected4× | Ratio | Significance |
|---|---|---|---|---|---|
| Organic acids and derivatives | 2 | 0.5 | 4.37× | not tested | |
| Homogeneous non-metal compounds | 2 | 0.6 | 3.14× | not tested | |
| Lipids and lipid-like molecules | 1 | 0.3 | 3.04× | not tested | |
| Homogeneous metal compounds | 3 | 1.5 | 2.07× | not tested |
Unit: a protein (UniProt accession) with a ligand-binding domain in this X-group, counted once per superclass. Expected counts use each superclass's frequency across all ligand-binding X-groups; significance is Fisher's exact test with Benjamini–Hochberg correction. Buffers and crystallization additives are excluded. ECOD v295.2; the method follows the ECOD 2027 update, whose published figures used a slightly different artifact filter.
DrugBank compounds
| DrugBank | PDB ligand | Name | Domains |
|---|---|---|---|
| DB02270 | DST | Dimethylallyl S-Thiolodiphosphate | 3 |
| DB04160 | PPV | Pyrophosphoric acid | 3 |
| DB01785 | DMA | Dimethylallyl Diphosphate | 2 |
Most frequently bound compounds
| PDB ligand | Name | Domains in contact |
|---|---|---|
| MGmetal | MAGNESIUM ION | 12 |
| ZNmetal | ZINC ION | 8 |
| DST | DIMETHYLALLYL S-THIOLODIPHOSPHATE | 3 |
| PPV | PYROPHOSPHATE | 3 |
| DMA | DIMETHYLALLYL DIPHOSPHATE | 2 |
| DPO | DIPHOSPHATE | 2 |
| CAmetal | CALCIUM ION | 1 |
| CL | CHLORIDE ION | 1 |