X-group (possible homology)
4967 helical bundle domain in reverse transcriptase-like polymerases
Ligands and drugs
3,414
Member domains
1,051
with ligand contacts (≤ 4 Å)
30.8% of members
881
with DrugDomain annotations
25.8% of members
465
with a DrugBank compound
13.6% 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.
84
Proteins with classified ligands
10
Superclasses bound (of 23)
8.6
Superclasses per 20 proteins
broader than 70% 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 |
|---|---|---|---|---|---|
| Benzenoids | 19 | 6.1 | 3.14× | q < 0.0001 | |
| Homogeneous metal compounds | 52 | 40.7 | 1.28× | q = 0.03 | |
| Organoheterocyclic compounds | 15 | 12.8 | 1.18× | q = 0.53 | |
| Organic acids and derivatives | 11 | 12.8 | 0.86× | q = 0.83 | |
| Nucleosides, nucleotides, and analogues | 18 | 22.9 | 0.79× | q = 0.34 | |
| Homogeneous non-metal compounds | 12 | 17.8 | 0.67× | q = 0.20 | |
| Organic oxygen compounds | 8 | 16.5 | 0.48× | q = 0.03 | |
| Lipids and lipid-like molecules | 0 | 9.2 | 0 | q = 4.1e-4 | |
| Phenylpropanoids and polyketides | 8 | 1.7 | 4.64× | not tested | |
| Organohalogen compounds | 1 | 0.2 | 4.24× | not tested | |
| Organic nitrogen compounds | 4 | 2.6 | 1.51× | 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 |
|---|---|---|---|
| DB04137 | GTP | Guanosine-5'-Triphosphate | 23 |
| DB00171 | ATP | ATP | 10 |
| DB01694 | TAR | D-tartaric acid | 6 |
| DB02431 | CTP | Cytidine-5'-Triphosphate | 6 |
| DB09459 | TLA | L-tartaric acid | 6 |
| DB02676 | B3P | 2-[3-(2-Hydroxy-1,1-Dihydroxymethyl-Ethylamino)-Propylamino]-2-Hydroxymethyl-Propane-1,3-Diol | 4 |
| DB04005 | UTP | Uridine 5'-triphosphate | 4 |
| DB08701 | VGI | 2-(3-BROMOPHENYL)-6-[(2-HYDROXYETHYL)AMINO]-1H-BENZO[DE]ISOQUINOLINE-1,3(2H)-DIONE | 4 |
| DB13095 | JT1 | JTK-853 | 4 |
| DB01972 | G | Guanosine-5'-Monophosphate | 3 |
| DB05884 | 2N5 | HCV-086 | 3 |
| DB07238 | 79Z | Nesbuvir | 3 |
| DB08279 | NN3 | 3-{ISOPROPYL[(TRANS-4-METHYLCYCLOHEXYL)CARBONYL]AMINO}-5-PHENYLTHIOPHENE-2-CARBOXYLIC ACID | 3 |
| DB00544 | URF | Fluorouracil | 2 |
| DB00811 | RBV | Ribavirin | 2 |
| DB02175 | MLA | Malonic acid | 2 |
| DB02331 | 154 | (2s)-2-[(5-Benzofuran-2-Yl-Thiophen-2-Ylmethyl)-(2,4-Dichloro-Benzoyl)-Amino]-3-Phenyl-Propionic Acid | 2 |
| DB02721 | PYZ | 4-Iodopyrazole | 2 |
| DB03605 | 153 | (2s)-2-[(2,4-Dichloro-Benzoyl)-(3-Trifluoromethyl-Benzyl)-Amino]-3-Phenyl-Propionic Acid | 2 |
| DB04555 | CDP | Cytidine-5'-Diphosphate | 2 |
Most frequently bound compounds
| PDB ligand | Name | Domains in contact |
|---|---|---|
| ZNmetal | ZINC ION | 195 |
| MGmetal | MAGNESIUM ION | 119 |
| MNmetal | MANGANESE (II) ION | 43 |
| 23E | (2E)-3-(4-{[(1-{[(13-cyclohexyl-6-oxo-6,7-dihydro-5H-indolo[1,2-d][1,4]benzodiazepin-10-yl)carbonyl]amino}cyclopentyl)carbonyl]amino}phenyl)prop-2-enoic acid | 32 |
| GTP | GUANOSINE-5'-TRIPHOSPHATE | 30 |
| CL | CHLORIDE ION | 29 |
| CDmetal | CADMIUM ION | 12 |
| ATP | ADENOSINE-5'-TRIPHOSPHATE | 11 |
| 1PV | [4-({[5-cyclopropyl-2-(4-fluorophenyl)-3-(methylcarbamoyl)-1-benzofuran-6-yl](methylsulfonyl)amino}methyl)-2-fluorophenyl]boronic acid | 7 |
| 2NG | 4-({4-methyl-3-[(3-nitrobenzoyl)amino]benzoyl}amino)naphthalene-1,5-disulfonic acid | 7 |
| CAmetal | CALCIUM ION | 6 |
| CTP | CYTIDINE-5'-TRIPHOSPHATE | 6 |
| IX6 | (11S)-10-[(2,5-dimethyl-1,3-oxazol-4-yl)carbonyl]-11-{2-fluoro-4-[(2-methylprop-2-en-1-yl)oxy]phenyl}-3,3-dimethyl-2,3,4,5,10,11-hexahydrothiopyrano[3,2-b][1,5]benzodiazepin-6-ol 1,1-dioxide | 5 |
| UTP | URIDINE 5'-TRIPHOSPHATE | 5 |
| 20V | 3-[(E)-{4-formyl-5-hydroxy-6-methyl-3-[(phosphonooxy)methyl]pyridin-2-yl}diazenyl]-7-nitronaphthalene-1,5-disulfonicacid | 4 |
| 3AE | 4-(trifluoromethyl)benzoic acid | 4 |
| 3AQ | (4-hydroxyphenyl)acetonitrile | 4 |
| 3B1 | (2R)-morpholin-4-yl(phenyl)ethanenitrile | 4 |
| 79Z | 5-cyclopropyl-2-(4-fluorophenyl)-6-[(2-hydroxyethyl)(methylsulfonyl)amino]-N-methyl-1-benzofuran-3-carboxamide | 4 |
| C9A | 4-chlorobenzyl 6-fluoro-7-(4-methylpiperazin-1-yl)-1-[4-(methylsulfonyl)benzyl]-4-oxo-1,4-dihydroquinoline-3-carboxylate | 4 |