4025 alpha-helical domain in nickel-iron hydrogenase, large subunit
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 |
|---|---|---|---|---|---|
| Homogeneous non-metal compounds | 15 | 5.7 | 2.62× | q = 3.0e-4 | |
| Homogeneous metal compounds | 9 | 13.1 | 0.69× | q = 0.18 | |
| Organic oxygen compounds | 1 | 5.3 | 0.19× | q = 0.08 | |
| Nucleosides, nucleotides, and analogues | 0 | 7.4 | 0 | q = 8.2e-4 | |
| Organic salts | 10 | 0.0 | 361× | not tested | |
| Mixed metal/non-metal compounds | 3 | 0.6 | 5.37× | not tested | |
| Organic nitrogen compounds | 3 | 0.9 | 3.53× | not tested | |
| Lipids and lipid-like molecules | 8 | 3.0 | 2.70× | not tested | |
| Phenylpropanoids and polyketides | 1 | 0.6 | 1.81× | not tested | |
| Organic acids and derivatives | 3 | 4.1 | 0.73× | not tested | |
| Benzenoids | 1 | 2.0 | 0.51× | not tested | |
| Organoheterocyclic compounds | 2 | 4.1 | 0.49× | 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 |
|---|---|---|---|
| DB09140 | OXY | Oxygen | 12 |
| DB11588 | CMO | Carbon monoxide | 10 |
| DB00145 | GLY | Glycine | 5 |
| DB02043 | LHG | 1,2-Dipalmitoyl-Phosphatidyl-Glycerole | 3 |
| DB03570 | 144 | Tris-Hydroxymethyl-Methyl-Ammonium | 3 |
| DB07640 | DCQ | 2-decyl-5,6-dimethoxy-3-methylcyclohexa-2,5-diene-1,4-dione | 3 |
| DB11457 | 970 | Rotenone | 2 |
| DB00157 | — | NADH | 1 |
| DB02219 | CXS | 3-(cyclohexylamino)propanesulfonic acid | 1 |
| DB02643 | C15 | N-Dodecyl-N,N-Dimethyl-3-Ammonio-1-Propanesulfonate | 1 |
| DB08689 | UQ1 | Ubiquinone Q1 | 1 |
Most frequently bound compounds
| PDB ligand | Name | Domains in contact |
|---|---|---|
| SF4 | IRON/SULFUR CLUSTER | 383 |
| F3S | FE3-S4 CLUSTER | 234 |
| CL | CHLORIDE ION | 51 |
| PC1 | 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE | 44 |
| 3PE | 1,2-Distearoyl-sn-glycerophosphoethanolamine | 37 |
| H2S | HYDROSULFURIC ACID | 28 |
| MGmetal | MAGNESIUM ION | 27 |
| 6ML | oxygen-damaged SF4 | 19 |
| FEmetal | FE (III) ION | 12 |
| SF3 | FE4-S3 CLUSTER | 9 |
| F4S | FE4-S3 CLUSTER | 7 |
| 970 | (2R,6aS,12aS)-8,9-dimethoxy-2-(prop-1-en-2-yl)-1,2,12,12a-tetrahydrofuro[2',3':7,8][1]benzopyrano[2,3-c][1]benzopyran-6(6aH)-one | 6 |
| ER2 | Fe4S4 | 6 |
| LImetal | LITHIUM ION | 6 |
| NAmetal | SODIUM ION | 6 |
| OXY | OXYGEN MOLECULE | 6 |
| U10 | UBIQUINONE-10 | 6 |
| FSX | BIS-(MU-2-OXO),[(MU-3--SULFIDO)-BIS(MU-2--SULFIDO)-TRIS(CYS-S)-TRI-IRON] (AQUA)(GLU-O)IRON(II) | 5 |
| GLY | GLYCINE | 5 |
| KR | KRYPTON | 5 |