X-group (possible homology)
1061 gp120 inner domain
Ligands and drugs
1,724
Member domains
1,278
with ligand contacts (≤ 4 Å)
74.1% of members
757
with DrugDomain annotations
43.9% of members
699
with a DrugBank compound
40.5% 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.
59
Proteins with classified ligands
8
Superclasses bound (of 23)
5.9
Superclasses per 20 proteins
narrower than 75% 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 | 59 | 11.6 | 5.09× | q < 0.0001 | |
| Organoheterocyclic compounds | 9 | 9.0 | 1.00× | q = 1.00 | |
| Organic acids and derivatives | 5 | 9.0 | 0.56× | q = 0.27 | |
| Lipids and lipid-like molecules | 3 | 6.5 | 0.46× | q = 0.28 | |
| Homogeneous non-metal compounds | 3 | 12.5 | 0.24× | q = 2.8e-3 | |
| Homogeneous metal compounds | 2 | 28.6 | 0.07× | q < 0.0001 | |
| Nucleosides, nucleotides, and analogues | 0 | 16.1 | 0 | q < 0.0001 | |
| Organosulfur compounds | 1 | 1.2 | 0.84× | not tested | |
| Benzenoids | 3 | 4.3 | 0.70× | 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 | 662 |
| DB14675 | 83J | Temsavir | 7 |
| DB02210 | HEZ | Hexane-1,6-Diol | 2 |
| DB00513 | ACA | Aminocaproic acid | 1 |
| DB02175 | MLA | Malonic acid | 1 |
| DB02379 | BGC | Beta-D-Glucose | 1 |
| DB04473 | FUC | alpha-L-fucose | 1 |
Most frequently bound compounds
| PDB ligand | Name | Domains in contact |
|---|---|---|
| NAG | 2-acetamido-2-deoxy-beta-D-glucopyranose | 1,254 |
| 83G | 1-[(2R)-4-(benzenecarbonyl)-2-methylpiperazin-1-yl]-2-(4-methoxy-1H-pyrrolo[2,3-b]pyridin-3-yl)ethane-1,2-dione | 32 |
| 7IT | N~1~-{(1R,2R,3S)-2-(carbamimidamidomethyl)-3-[(3S)-3,4-dihydroxybutyl]-5-[(methylamino)methyl]-2,3-dihydro-1H-inden-1-yl}-N~2~-(4-chloro-3-fluorophenyl)ethanediamide | 12 |
| 5VG | ~{N}'-[(1~{R},2~{R})-2-(carbamimidamidomethyl)-5-(methylaminomethyl)-2,3-dihydro-1~{H}-inden-1-yl]-~{N}-(4-chloranyl-3-fluoranyl-phenyl)ethanediamide | 8 |
| 7IW | N~1~-{(1R,2R,3S)-2-(carbamimidamidomethyl)-3-[(3R)-3,4-dihydroxybutyl]-5-[(methylamino)methyl]-2,3-dihydro-1H-inden-1-yl}-N~2~-(4-chloro-3-fluorophenyl)ethanediamide | 8 |
| 83J | 1-[4-(benzenecarbonyl)piperazin-1-yl]-2-[4-methoxy-7-(3-methyl-1H-1,2,4-triazol-1-yl)-1H-pyrrolo[2,3-c]pyridin-3-yl]ethane-1,2-dione | 7 |
| Y26 | propyl (2R,3S)-2-(carbamimidamidomethyl)-3-[2-(4-chloro-3-fluoroanilino)(oxo)acetamido]-6-[(methylamino)methyl]-2,3-dihydro-1H-indole-1-carboxylate | 7 |
| NAmetal | SODIUM ION | 5 |
| 1C1 | amino({[(1R,2R)-1-({[(4-chloro-3-fluorophenyl)amino](oxo)acetyl}amino)-2,3-dihydro-1H-inden-2-yl]methyl}amino)methaniminium | 4 |
| 3ZM | 5-(4-chlorophenyl)-N-{(S)-[5-(hydroxymethyl)-4-methyl-1,3-thiazol-2-yl][(2R)-piperidin-2-yl]methyl}-1H-pyrrole-2-carboxamide | 4 |
| I6M | N~1~-[(1R,2R)-2-(carbamimidamidomethyl)-5-{[(2R)-2-(hydroxymethyl)pyrrolidin-1-yl]methyl}-2,3-dihydro-1H-inden-1-yl]-N~2~-(4-chloro-3-fluorophenyl)ethanediamide | 4 |
| I6Q | N~1~-[(1R,2R)-5-{[(3R)-3-aminopyrrolidin-1-yl]methyl}-2-(carbamimidamidomethyl)-2,3-dihydro-1H-inden-1-yl]-N~2~-(4-chloro-3-fluorophenyl)ethanediamide | 4 |
| Y1O | methyl (2R,3S)-2-(carbamimidamidomethyl)-3-[2-(4-chloro-3-fluoroanilino)(oxo)acetamido]-6-[(methylamino)methyl]-2,3-dihydro-1H-indole-1-carboxylate | 4 |
| Y1T | (pentafluorophenyl)methyl (2R,3S)-2-(carbamimidamidomethyl)-3-[2-(4-chloro-3-fluoroanilino)(oxo)acetamido]-6-[(methylamino)methyl]-2,3-dihydro-1H-indole-1-carboxylate | 4 |
| Y1X | ethyl (2R,3S)-2-(carbamimidamidomethyl)-3-[2-(4-chloro-3-fluoroanilino)(oxo)acetamido]-6-[(methylamino)methyl]-2,3-dihydro-1H-indole-1-carboxylate | 4 |
| Y2E | 3,3,3-trifluoropropyl (2R,3S)-2-(carbamimidamidomethyl)-3-[2-(4-chloro-3-fluoroanilino)(oxo)acetamido]-6-[(methylamino)methyl]-2,3-dihydro-1H-indole-1-carboxylate | 4 |
| Y2K | 2,2,2-trifluoroethyl (2R,3S)-2-(carbamimidamidomethyl)-3-[2-(4-chloro-3-fluoroanilino)(oxo)acetamido]-6-[(methylamino)methyl]-2,3-dihydro-1H-indole-1-carboxylate | 4 |
| Y2O | benzyl (2R,3S)-2-(carbamimidamidomethyl)-3-[2-(4-chloro-3-fluoroanilino)(oxo)acetamido]-6-[(methylamino)methyl]-2,3-dihydro-1H-indole-1-carboxylate | 4 |
| 0LY | N-(4-bromophenyl)-N'-(2,2,6,6-tetramethylpiperidin-4-yl)ethanediamide | 3 |
| CL | CHLORIDE ION | 3 |