X-group (possible homology)
385 Cystine-knot cytokines
Ligands and drugs
1,759
Member domains
338
with ligand contacts (≤ 4 Å)
19.2% of members
285
with DrugDomain annotations
16.2% of members
210
with a DrugBank compound
11.9% of members
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.
40
Proteins with classified ligands
9
Superclasses bound (of 23)
6.7
Superclasses per 20 proteins
narrower than 65% of the 256 X-groups with enough proteins to compare (median 7.6)
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 oxygen compounds | 28 | 7.9 | 3.56× | q < 0.0001 | |
| Homogeneous non-metal compounds | 13 | 8.5 | 1.53× | q = 0.13 | |
| Organic acids and derivatives | 4 | 6.1 | 0.66× | q = 0.59 | |
| Homogeneous metal compounds | 10 | 19.4 | 0.52× | q = 8.0e-3 | |
| Organoheterocyclic compounds | 1 | 6.1 | 0.17× | q = 0.04 | |
| Nucleosides, nucleotides, and analogues | 0 | 10.9 | 0 | q < 0.0001 | |
| Phenylpropanoids and polyketides | 1 | 0.8 | 1.22× | not tested | |
| Organic nitrogen compounds | 1 | 1.3 | 0.80× | not tested | |
| Lipids and lipid-like molecules | 2 | 4.4 | 0.46× | not tested | |
| Benzenoids | 1 | 2.9 | 0.35× | not tested |
enriched (q < 0.05)depleted (q < 0.05)not significantnot tested (expected < 5)
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 |
|---|---|---|---|
| DB00141 | NAG | N-Acetylglucosamine | 76 |
| DB00143 | GSH | Glutathione | 4 |
| DB02042 | 1PG | 2-(2-{2-[2-(2-Methoxy-Ethoxy)-Ethoxy]-Ethoxy}-Ethoxy)-Ethanol | 3 |
| DB01694 | TAR | D-tartaric acid | 2 |
| DB02175 | MLA | Malonic acid | 2 |
| DB02676 | B3P | 2-[3-(2-Hydroxy-1,1-Dihydroxymethyl-Ethylamino)-Propylamino]-2-Hydroxymethyl-Propane-1,3-Diol | 2 |
| DB01017 | — | Minocycline | 1 |
| DB01034 | — | Cerulenin | 1 |
| DB01083 | — | — | 1 |
| DB01120 | — | Gliclazide | 1 |
| DB01136 | — | — | 1 |
| DB01373 | — | — | 1 |
| DB01407 | — | — | 1 |
| DB01593 | — | — | 1 |
| DB03088 | — | Pidolic acid | 1 |
| DB03556 | PE5 | 2-(2-{2-[2-(2-{2-[2-(2-Ethoxy-Ethoxy)-Ethoxy]-Ethoxy}-Ethoxy)-Ethoxy]-Ethoxy}-Ethoxy)-Ethanol, Polyethyleneglycol Peg400 | 1 |
| DB03912 | PNS | D-pantetheine 4'-phosphate | 1 |
| DB05047 | — | — | 1 |
| DB05294 | — | Vandetanib | 1 |
| DB05434 | — | — | 1 |
Most frequently bound compounds
| PDB ligand | Name | Domains in contact |
|---|---|---|
| NAG | 2-acetamido-2-deoxy-beta-D-glucopyranose | 70 |
| CL | CHLORIDE ION | 31 |
| NAmetal | SODIUM ION | 14 |
| TFA | trifluoroacetic acid | 10 |
| CAmetal | CALCIUM ION | 8 |
| ZNmetal | ZINC ION | 8 |
| A1CXF | (3S)-N-[(3-{[(1S)-2-anilino-1-cyclohexyl-2-oxoethyl]carbamoyl}phenyl)methyl]-2,2-dimethylthiomorpholine-3-carboxamide | 4 |
| A1ISG | (E)-N-[(1S)-1-[4,4-bis(fluoranyl)cyclohexyl]-2-oxidanylidene-2-[[5-[[(4S)-2-oxidanylidene-4-(trifluoromethyl)imidazolidin-1-yl]methyl]-1,3-thiazol-2-yl]amino]ethyl]-3-cyclopropyl-2-fluoranyl-prop-2-enamide | 4 |
| A1JPQ | ~{N}-[(~{S})-[3-[[(6~{R})-3-bromanyl-5,6,7,8-tetrahydroimidazo[1,2-a]pyridin-6-yl]methyl]-1~{H}-1,2,4-triazol-5-yl]-cyclohexyl-methyl]-4-methyl-1,2,5-oxadiazole-3-carboxamide | 4 |
| A1JPS | ~{N}-[(~{S})-cyclohexyl-[3-[(4-oxidanylidene-3~{H}-phthalazin-1-yl)methyl]-1~{H}-1,2,4-triazol-5-yl]methyl]-4-methyl-1,2,5-oxadiazole-3-carboxamide | 4 |
| BEN | BENZAMIDINE | 4 |
| GSH | Glutathione | 4 |
| RMQ | (3~{R})-4-[4-[[(2~{S})-2-[[2,2-bis(fluoranyl)-2-phenyl-ethanoyl]amino]-3-(2-chlorophenyl)propanoyl]amino]phenyl]-3-[[(2~{S})-3-methyl-2-[2-[2-[(2-methylpropan-2-yl)oxycarbonylamino]ethoxy]ethanoylamino]butanoyl]amino]butanoic acid | 4 |
| S12 | O-[(S)-hydroxy{[(2S)-2-hydroxy-3-(octadec-9-enoyloxy)propyl]oxy}phosphoryl]-L-serine | 4 |
| 1PG | 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL | 3 |
| CSmetal | CESIUM ION | 3 |
| I5M | 5'-deoxy-5'-({(2S)-2-({2-[(N-{(2R)-4-[(dioxo-lambda~5~-phosphanyl)oxy]-2-hydroxy-3,3-dimethylbutanoyl}-beta-alanyl)amino]ethyl}sulfanyl)-2-[(2S)-pyrrolidin-2-yl]ethanesulfonyl}amino)adenosine | 3 |
| XCE | ~{N}-[(2~{S})-1-[[(1~{S})-1-(8~{a}~{H}-imidazo[1,2-a]pyrimidin-2-yl)ethyl]amino]-1-oxidanylidene-4-phenyl-butan-2-yl]-4,5-bis(chloranyl)-1~{H}-pyrrole-2-carboxamide | 3 |
| 63O | N-(4-{2-[({1-[2-(dimethylamino)-2-oxoethyl]cyclopentyl}acetyl)amino]ethyl}phenyl)-2-fluoro-Nalpha-[(1-methyl-1H-pyrazol-5-yl)carbonyl]-L-phenylalaninamide | 2 |
| 63P | (9'S,17'R)-6'-chloro-N-methyl-9'-{[(1-methyl-1H-pyrazol-5-yl)carbonyl]amino}-10',19'-dioxo-2'-oxa-11',18'-diazaspiro[cyclopentane-1,21'-tetracyclo[20.2.2.2~12,15~.1~3,7~]nonacosane]-1'(24'),3'(29'),4',6',12',14',22',25',27'-nonaene-17'-carboxamide | 2 |