X-group (possible homology)
5000 Toxins' membrane translocation domains
Ligands and drugs
1,511
Member domains
663
with ligand contacts (≤ 4 Å)
43.9% of members
573
with DrugDomain annotations
37.9% of members
242
with a DrugBank compound
16.0% 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.
27
Proteins with classified ligands
12
Superclasses bound (of 23)
10.9
Superclasses per 20 proteins
broader than 98% 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 |
|---|---|---|---|---|---|
| Homogeneous non-metal compounds | 18 | 5.7 | 3.14× | q < 0.0001 | |
| Organic oxygen compounds | 6 | 5.3 | 1.13× | q = 0.87 | |
| Homogeneous metal compounds | 10 | 13.1 | 0.77× | q = 0.33 | |
| Nucleosides, nucleotides, and analogues | 1 | 7.4 | 0.14× | q = 8.0e-3 | |
| Organometallic compounds | 1 | 0.0 | 26× | not tested | |
| Phenylpropanoids and polyketides | 4 | 0.6 | 7.22× | not tested | |
| Hydrocarbons | 1 | 0.2 | 5.38× | not tested | |
| Benzenoids | 6 | 2.0 | 3.08× | not tested | |
| Organic nitrogen compounds | 2 | 0.9 | 2.35× | not tested | |
| Organoheterocyclic compounds | 6 | 4.1 | 1.47× | not tested | |
| Organic acids and derivatives | 5 | 4.1 | 1.21× | not tested | |
| Lipids and lipid-like molecules | 1 | 3.0 | 0.34× | 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 |
|---|---|---|---|
| DB12340 | 1XJ | Navitoclax | 16 |
| DB17023 | N3C | ABT-737 | 8 |
| DB04327 | PEE | Phosphatidylethanolamine | 6 |
| DB11581 | LBM | Venetoclax | 5 |
| DB18365 | F3Q | S-55746 | 3 |
| DB01694 | TAR | D-tartaric acid | 2 |
| DB02042 | 1PG | 2-(2-{2-[2-(2-Methoxy-Ethoxy)-Ethoxy]-Ethoxy}-Ethoxy)-Ethanol | 2 |
| DB02676 | B3P | 2-[3-(2-Hydroxy-1,1-Dihydroxymethyl-Ethylamino)-Propylamino]-2-Hydroxymethyl-Propane-1,3-Diol | 2 |
| DB01050 | — | — | 1 |
| DB01229 | — | Paclitaxel | 1 |
| DB01248 | — | Docetaxel | 1 |
| DB01367 | — | Rasagiline | 1 |
| DB02580 | PG6 | Pentaglyme | 1 |
| DB02774 | PDO | 1,3-Propanediol | 1 |
| DB02994 | CAD | Cacodylic acid | 1 |
| DB03309 | NHE | N-cyclohexyltaurine | 1 |
| DB03627 | ADM | Adamantane | 1 |
| DB05103 | — | — | 1 |
| DB05297 | — | — | 1 |
| DB06307 | — | — | 1 |
Most frequently bound compounds
| PDB ligand | Name | Domains in contact |
|---|---|---|
| CL | CHLORIDE ION | 39 |
| ZNmetal | ZINC ION | 39 |
| 1XJ | 4-(4-{[2-(4-chlorophenyl)-5,5-dimethylcyclohex-1-en-1-yl]methyl}piperazin-1-yl)-N-[(4-{[(2R)-4-(morpholin-4-yl)-1-(phenylsulfanyl)butan-2-yl]amino}-3-[(trifluoromethyl)sulfonyl]phenyl)sulfonyl]benzamide | 15 |
| CUmetal | COPPER (II) ION | 13 |
| 19G | 3-[3-(4-chloro-3,5-dimethylphenoxy)propyl]-1-benzothiophene-2-carboxylic acid | 12 |
| 4M6 | 1-[3-(naphthalen-1-yloxy)propyl]-5,6-dihydro-4H-pyrrolo[3,2,1-ij]quinoline-2-carboxylic acid | 12 |
| 4M7 | (1R)-7-[3-(naphthalen-1-yloxy)propyl]-3,4-dihydro-2H-[1,4]thiazepino[2,3,4-hi]indole-6-carboxylic acid 1-oxide | 12 |
| 8SP | O-[(R)-{[(2R)-2,3-bis(octanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine | 12 |
| NAmetal | SODIUM ION | 12 |
| QHP | (R)-2-(3-([1,1'-Biphenyl]-4-carbonyl)-3-(4-methylbenzyl)ureido)-3-(((3R,5R,7R)-adamantan-1-ylmethyl)sulfonyl)propanoic acid | 12 |
| QHS | (R)-2-(3-([1,1'-Biphenyl]-4-carbonyl)-3-(4-methylbenzyl)ureido)-3-((cyclohexylmethyl)sulfonyl)propanoic acid | 12 |
| 6AK | 4-{8-chloro-11-[3-(4-chloro-3,5-dimethylphenoxy)propyl]-1-oxo-7-(1,3,5-trimethyl-1H-pyrazol-4-yl)-4,5-dihydro-1H-[1,4]diazepino[1,2-a]indol-2(3H)-yl}-1-methyl-1H-indole-6-carboxylic acid | 10 |
| 38H | 2-[8-(1,3-benzothiazol-2-ylcarbamoyl)-3,4-dihydroisoquinolin-2(1H)-yl]-5-{3-[4-(1H-pyrazolo[3,4-d]pyrimidin-1-yl)phenoxy]propyl}-1,3-thiazole-4-carboxylic acid | 8 |
| BR | BROMIDE ION | 8 |
| CAmetal | CALCIUM ION | 8 |
| CDmetal | CADMIUM ION | 8 |
| LC6 | 7-(4-{[(4-{[(2R)-4-(dimethylamino)-1-(phenylsulfanyl)butan-2-yl]amino}-3-nitrophenyl)sulfonyl]carbamoyl}-2-methylphenyl)-3-[3-(naphthalen-1-yloxy)propyl]pyrazolo[1,5-a]pyridine-2-carboxylic acid | 8 |
| N3C | 4-{4-[(4'-CHLOROBIPHENYL-2-YL)METHYL]PIPERAZIN-1-YL}-N-{[4-({(1R)-3-(DIMETHYLAMINO)-1-[(PHENYLTHIO)METHYL]PROPYL}AMINO)-3-NITROPHENYL]SULFONYL}BENZAMIDE | 8 |
| PG8 | 1,2-DIOCTANOYL-SN-GLYCERO-3-[PHOSPHO-RAC-(1-GLYCEROL) | 8 |
| 19H | 6-chloro-3-[3-(4-chloro-3,5-dimethylphenoxy)propyl]-1H-indole-2-carboxylic acid | 7 |