X-group (possible homology)
178 SWIB/MDM2 domain
Ligands and drugs
565
Member domains
245
with ligand contacts (≤ 4 Å)
43.4% of members
250
with DrugDomain annotations
44.2% of members
112
with a DrugBank compound
19.8% 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.
6
Proteins with classified ligands
9
Superclasses bound (of 23)
—
Superclasses per 20 proteins
fewer than 20 proteins: too few to compare at equal depth
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 |
|---|---|---|---|---|---|
| Phenylpropanoids and polyketides | 4 | 0.1 | 33× | not tested | |
| Organic nitrogen compounds | 2 | 0.2 | 11× | not tested | |
| Organosulfur compounds | 1 | 0.1 | 8.22× | not tested | |
| Benzenoids | 3 | 0.4 | 6.94× | not tested | |
| Organoheterocyclic compounds | 4 | 0.9 | 4.39× | not tested | |
| Organic oxygen compounds | 3 | 1.2 | 2.55× | not tested | |
| Organic acids and derivatives | 2 | 0.9 | 2.19× | not tested | |
| Homogeneous non-metal compounds | 2 | 1.3 | 1.57× | not tested | |
| Homogeneous metal compounds | 3 | 2.9 | 1.03× | 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 |
|---|---|---|---|
| DB17039 | NUT | Nutlin-3 | 14 |
| DB12541 | 7HC | SAR-405838 | 5 |
| DB00536 | GAI | Guanidine | 3 |
| DB02872 | IMZ | Cis-[4,5-Bis-(4-Bromophenyl)-2-(2-Ethoxy-4-Methoxyphenyl)-4,5-Dihydroimidazol-1-Yl]-[4-(2-Hydroxyethyl)Piperazin-1-Yl]Methanone | 3 |
| DB04144 | IMY | Cis-[4,5-Bis-(4-Chlorophenyl)-2-(2-Isopropoxy-4-Methoxyphenyl)-4,5-Dihyd Roimidazol-1-Yl]-Piperazin-1-Yl-Methanone | 2 |
| DB01593 | — | — | 1 |
| DB03345 | BME | Mercaptoethanol | 1 |
| DB03434 | MPO | 3-(N-morpholino)propanesulfonic acid | 1 |
| DB14487 | — | — | 1 |
| DB14533 | — | — | 1 |
| DB14793 | 1F0 | RO-5045337 | 1 |
| DB16331 | 9QW | Siremadlin | 1 |
Most frequently bound compounds
| PDB ligand | Name | Domains in contact |
|---|---|---|
| CL | CHLORIDE ION | 32 |
| O4B | 1,4,7,10,13,16-HEXAOXACYCLOOCTADECANE | 19 |
| NUT | 4-({(4S,5R)-4,5-bis(4-chlorophenyl)-2-[4-methoxy-2-(propan-2-yloxy)phenyl]-4,5-dihydro-1H-imidazol-1-yl}carbonyl)piperazin-2-one | 14 |
| 03M | (5Z)-5-[(6-chloro-7-methyl-1H-indol-3-yl)methylidene]-3-(3,4-difluorobenzyl)imidazolidine-2,4-dione | 8 |
| 0Y7 | {(3R,5R,6S)-5-(3-chlorophenyl)-6-(4-chlorophenyl)-1-[(2S)-1-hydroxybutan-2-yl]-2-oxopiperidin-3-yl}acetic acid | 8 |
| 6GG | 4-({6-[(6-chloro-3-{1-[(4-chlorophenyl)methyl]-4-(4-fluorophenyl)-1H-imidazol-5-yl}-1H-indole-2-carbonyl)oxy]hexyl}amino)-4-oxobutanoic acid | 8 |
| WHL | N,N'-(1,4-phenylene)diacetamide | 7 |
| 35T | {(3R,5R,6S)-5-(3-chlorophenyl)-6-(4-chlorophenyl)-1-[(1S)-1-cyclopropyl-2-(pyrrolidin-1-ylsulfonyl)ethyl]-3-methyl-2-oxopiperidin-3-yl}acetic acid | 6 |
| 6SS | (3~{S},3'~{S},4'~{S},5'~{S})-4'-azanyl-6-chloranyl-3'-(3-chloranyl-2-fluoranyl-phenyl)-1'-[(3-ethoxyphenyl)methyl]-5'-methyl-spiro[1~{H}-indole-3,2'-pyrrolidine]-2-one | 6 |
| 7HC | (2'S,3R,4'S,5'R)-6-chloro-4'-(3-chloro-2-fluorophenyl)-2'-(2,2-dimethylpropyl)-N-(trans-4-hydroxycyclohexyl)-2-oxo-1,2-dihydrospiro[indole-3,3'-pyrrolidine]-5'-carboxamide | 5 |
| 2V8 | 1-(5-chloro-2-methylphenyl)-5-(3-chlorophenyl)-2-(3-methylphenyl)-1H-imidazole-4-carboxylic acid | 4 |
| HUE | 6-chloranyl-3-[3-[(1~{S})-1-(4-chlorophenyl)ethyl]-5-phenyl-imidazol-4-yl]-~{N}-[2-(4-cyclohexylpiperazin-1-yl)ethyl]-1~{H}-indole-2-carboxamide | 4 |
| NAmetal | SODIUM ION | 4 |
| 0R3 | {(3R,5R,6S)-5-(3-chlorophenyl)-6-(4-chlorophenyl)-1-[(2S,3S)-2-hydroxypentan-3-yl]-3-methyl-2-oxopiperidin-3-yl}acetic acid | 3 |
| 1MT | (2'S,3R,4'S,5'R)-N-(2-aminoethyl)-6-chloro-4'-(3-chloro-2-fluorophenyl)-2'-(2,2-dimethylpropyl)-2-oxo-1,2-dihydrospiro[indole-3,3'-pyrrolidine]-5'-carboxamide | 3 |
| 1MY | {(2S,5R,6S)-6-(3-chlorophenyl)-5-(4-chlorophenyl)-4-[(2S)-1-hydroxybutan-2-yl]-3-oxomorpholin-2-yl}acetic acid | 3 |
| 20W | (2S,3R,4R,5R)-N-(4-carbamoyl-2-methoxyphenyl)-2'-chloro-4-(3-chloro-2-fluorophenyl)-2-(2,2-dimethylpropyl)-5'-oxo-4',5'-dihydrospiro[pyrrolidine-3,6'-thieno[3,2-b]pyrrole]-5-carboxamide | 3 |
| 2SW | [(3R,5R,6S)-1-[(2S)-1-(tert-butylsulfonyl)butan-2-yl]-5-(3-chlorophenyl)-6-(4-chlorophenyl)-3-methyl-2-oxopiperidin-3-yl]acetic acid | 3 |
| 2TW | [(2R,5R,6R)-4-[(1S)-2-(tert-butylsulfonyl)-1-cyclopropylethyl]-6-(3-chlorophenyl)-5-(4-chlorophenyl)-3-oxomorpholin-2-yl]acetic acid | 3 |
| 2TZ | [(2R,5R,6R)-4-[(2S)-1-(tert-butylsulfonyl)butan-2-yl]-6-(3-chlorophenyl)-5-(4-chlorophenyl)-3-oxomorpholin-2-yl]acetic acid | 3 |