4091 L,D-transpeptidase catalytic domain-like
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 metal compounds | 5 | 7.3 | 0.69× | q = 0.38 | |
| Organic salts | 2 | 0.0 | 130× | not tested | |
| Organosulfur compounds | 3 | 0.3 | 9.86× | not tested | |
| Benzenoids | 5 | 1.1 | 4.62× | not tested | |
| Organic acids and derivatives | 9 | 2.3 | 3.93× | not tested | |
| Organic nitrogen compounds | 1 | 0.5 | 2.12× | not tested | |
| Organic oxygen compounds | 5 | 3.0 | 1.70× | not tested | |
| Homogeneous non-metal compounds | 4 | 3.2 | 1.26× | not tested | |
| Organoheterocyclic compounds | 2 | 2.3 | 0.88× | 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 |
|---|---|---|---|
| DB02517 | DGL | D-Glutamic Acid | 4 |
| DB03345 | BME | Mercaptoethanol | 4 |
| DB00142 | GLU | Glutamic acid | 3 |
| DB01786 | DAL | D-Alanine | 2 |
| DB02343 | P3G | 3,6,9,12,15-Pentaoxaheptadecane | 2 |
| DB02763 | MNB | 5-Mercapto-2-Nitro-Benzoic Acid | 2 |
| DB03174 | POA | Phosphonoacetaldehyde | 2 |
| DB02379 | BGC | Beta-D-Glucose | 1 |
| DB02731 | EMT | Ethylmercurithiosalicylic acid | 1 |
| DB04237 | TAM | Tris(Hydroxyethyl)Aminomethane | 1 |
Most frequently bound compounds
| PDB ligand | Name | Domains in contact |
|---|---|---|
| CL | CHLORIDE ION | 13 |
| CDmetal | CADMIUM ION | 10 |
| IM2 | (5R)-5-[(1S,2R)-1-formyl-2-hydroxypropyl]-3-[(2-{[(E)-iminomethyl]amino}ethyl)sulfanyl]-4,5-dihydro-1H-pyrrole-2-carboxylic acid | 8 |
| NAmetal | SODIUM ION | 6 |
| 0JC | Di-mu-iodobis(ethylenediamine)diplatinum(II) | 4 |
| 2RG | (2S,3R,4S)-4-({(3S,5S)-5-[(3-carboxyphenyl)carbamoyl]pyrrolidin-3-yl}sulfanyl)-2-[(1S,2R)-1-formyl-2-hydroxypropyl]-3-methyl-3,4-dihydro-2H-pyrrole-5-carboxylic acid | 4 |
| 58U | (4S)-4-methyl-2,5,7-trioxoheptanoic acid | 4 |
| 6CL | 6-CARBOXYLYSINE | 4 |
| BME | BETA-MERCAPTOETHANOL | 4 |
| DGL | D-GLUTAMIC ACID | 4 |
| DWZ | (2S,3R,4S)-4-{[(3S,5S)-5-(dimethylcarbamoyl)pyrrolidin-3-yl]sulfanyl}-2-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-3-methyl-3,4-dihydro-2H-pyrrole-5-carboxylic acid | 4 |
| MXR | (2S,3R,4S)-4-{[(3S,5R)-5-(dimethylcarbamoyl)pyrrolidin-3-yl]sulfanyl}-2-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-3-methyl-3,4-dihydro-2H-pyrrole-5-carboxylic acid | 4 |
| 1RG | (4R,5S)-3-({(3S,5S)-5-[(3-carboxyphenyl)carbamoyl]pyrrolidin-3-yl}sulfanyl)-5-[(1S,2R)-1-formyl-2-hydroxypropyl]-4-methyl-4,5-dihydro-1H-pyrrole-2-carboxylic acid | 3 |
| 6B7 | (2~{R},3~{R},4~{R})-4-methyl-3-(2-oxidanylidene-2-propoxy-ethyl)sulfanyl-5-[(2~{S},3~{R})-3-oxidanyl-1-oxidanylidene-butan-2-yl]-3,4-dihydro-2~{H}-pyrrole-2-carboxylic acid | 3 |
| CAmetal | CALCIUM ION | 3 |
| DAL | D-ALANINE | 3 |
| GLU | GLUTAMIC ACID | 3 |
| NXL | (2S,5R)-1-formyl-5-[(sulfooxy)amino]piperidine-2-carboxamide | 3 |
| 5KO | (3R)-3-hydroxybutanal | 2 |
| 6QR | (2~{S},3~{R},4~{R})-4-(1~{H}-indol-3-ylsulfanyl)-3-methyl-2-[(2~{S},3~{S})-3-oxidanyl-1-oxidanylidene-butan-2-yl]-3,4-dihydro-2~{H}-pyrrole-5-carboxylic acid | 2 |