X-group (possible homology)
170 Retrovirus capsid protein
Ligands and drugs
10,415
Member domains
706
with ligand contacts (≤ 4 Å)
6.8% of members
282
with DrugDomain annotations
2.7% of members
119
with a DrugBank compound
1.1% 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.
18
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 |
|---|---|---|---|---|---|
| Homogeneous metal compounds | 5 | 8.7 | 0.57× | q = 0.15 | |
| Homogeneous non-metal compounds | 11 | 3.8 | 2.88× | not tested | |
| Organosulfur compounds | 1 | 0.4 | 2.74× | not tested | |
| Benzenoids | 3 | 1.3 | 2.31× | not tested | |
| Organic oxygen compounds | 8 | 3.5 | 2.26× | not tested | |
| Organic acids and derivatives | 6 | 2.8 | 2.19× | not tested | |
| Organoheterocyclic compounds | 2 | 2.7 | 0.73× | not tested | |
| Nucleosides, nucleotides, and analogues | 3 | 4.9 | 0.61× | not tested | |
| Lipids and lipid-like molecules | 1 | 2.0 | 0.51× | 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 |
|---|---|---|---|
| DB14981 | IHP | Phytic acid | 44 |
| DB15673 | QNG | Lenacapavir | 15 |
| DB06581 | 2I4 | Bevirimat | 6 |
| DB00693 | FLU | Fluorescein | 5 |
| DB00145 | GLY | Glycine | 2 |
| DB08027 | JPR | CAP-1 | 2 |
| DB00160 | ALA | Alanine | 1 |
| DB00171 | ATP | ATP | 1 |
| DB01681 | BHC | Benzene Hexacarboxylic Acid | 1 |
| DB02175 | MLA | Malonic acid | 1 |
| DB03222 | DTP | dATP | 1 |
| DB03345 | BME | Mercaptoethanol | 1 |
| DB14128 | NAD | Nadide | 1 |
Most frequently bound compounds
| PDB ligand | Name | Domains in contact |
|---|---|---|
| IHP | INOSITOL HEXAKISPHOSPHATE | 181 |
| CL | CHLORIDE ION | 131 |
| IOD | IODIDE ION | 104 |
| QNG | Lenacapavir | 74 |
| 2I4 | 3alpha-[(3-carboxy-3-methylbutanoyl)oxy]-8alpha,9beta,10alpha,13alpha,17alpha,19beta-lup-20(29)-en-28-oic acid | 30 |
| A1CH4 | 3,5-difluoro-Nalpha-[(5-hydroxy-1H-indol-3-yl)acetyl]-N-(4-methoxyphenyl)-N-methyl-L-phenylalaninamide | 24 |
| A1CH5 | N-[(1S)-1-[3-(4-chlorophenyl)pyridin-2-yl]-2-(3,5-difluorophenyl)ethyl]-2-(5-hydroxy-1H-indol-3-yl)acetamide | 24 |
| A1CH7 | N-methyl-N-phenyl-3-(pyridin-3-yl)-N~2~-{[3-(trifluoromethyl)-4,5,6,7-tetrahydro-1H-indazol-1-yl]acetyl}-L-alaninamide | 24 |
| J6U | 2-[4-(4-aminobenzene-1-sulfonyl)-2-oxopiperazin-1-yl]-N-[(1R)-2-(3,5-difluorophenyl)-1-{3-[4-(morpholine-4-sulfonyl)phenyl]-4-oxo-3,4-dihydroquinazolin-2-yl}ethyl]acetamide | 24 |
| K3L | 2-[4-(4-aminobenzene-1-sulfonyl)-2-oxopiperazin-1-yl]-N-{(1R)-2-(3,5-difluorophenyl)-1-[3-(4-methoxyphenyl)-4-oxo-3,4-dihydroquinazolin-2-yl]ethyl}acetamide | 24 |
| 1B0 | N-METHYL-NALPHA-[(2-METHYL-1H-INDOL-3-YL)ACETYL]-N-PHENYL-L-PHENYLALANINAMIDE | 20 |
| A1AAO | N-[(1S)-1-{(3M)-3-{4-chloro-3-[(cyclopropanesulfonyl)amino]-1-(2,2-difluoroethyl)-1H-indazol-7-yl}-6-[3-(methanesulfonyl)-3-methylbut-1-yn-1-yl]pyridin-2-yl}-2-(3,5-difluorophenyl)ethyl]-2-[(3bS,4aR)-3-(difluoromethyl)-5,5-difluoro-3b,4,4a,5-tetrahydro-1H-cyclopropa[3,4]cyclopenta[1,2-c]pyrazol-1-yl]acetamide | 20 |
| NAmetal | SODIUM ION | 13 |
| A1CCZ | 1-{(2S)-2-(4-tert-butylphenyl)-2-[(2,3-dihydro-1H-inden-2-yl)amino]ethyl}-3-(trifluoromethyl)pyridin-2(1H)-one | 12 |
| A1CH6 | (5M)-5-{2-[(1S)-2-(3,5-difluorophenyl)-1-{2-[(3bS,4aR)-5,5-difluoro-3-(trifluoromethyl)-3b,4,4a,5-tetrahydro-1H-cyclopropa[3,4]cyclopenta[1,2-c]pyrazol-1-yl]acetamido}ethyl]pyridin-3-yl}-2-fluorobenzamide | 12 |
| XBQ | Nalpha-{[4-(4-aminobenzene-1-sulfonyl)-2-oxopiperazin-1-yl]acetyl}-N-(4-methoxyphenyl)-N-methyl-L-phenylalaninamide | 12 |
| A1CCY | 1-{(2R)-2-(4-tert-butylphenyl)-2-[(2,3-dihydro-1H-inden-2-yl)amino]ethyl}-3-(trifluoromethyl)pyridin-2(1H)-one | 8 |
| 0OE | 4-{2-[5-(3-chlorophenyl)-1H-pyrazol-4-yl]-1-[3-(1H-imidazol-1-yl)propyl]-1H-benzimidazol-5-yl}benzoic acid | 5 |
| FLU | 2-(6-HYDROXY-3-OXO-3H-XANTHEN-9-YL)-BENZOIC ACID | 5 |
| A1ADQ | N-[(1S)-1-[(3P,7M)-3-{4-chloro-3-[(ethanesulfonyl)amino]-1-(2,2,2-trifluoroethyl)-1H-indazol-7-yl}-7-(3-fluoro-4-formylphenyl)-4-oxo-3,4-dihydroquinazolin-2-yl]-2-(3,5-difluorophenyl)ethyl]-2-[3-(trifluoromethyl)-5,6-dihydrocyclopenta[c]pyrazol-1(4H)-yl]acetamide | 4 |