X-group (possible homology)

7517 Nucleoside hydrolase

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Ligands and drugs

378

Member domains

180

with ligand contacts (≤ 4 Å)

47.6% of members

174

with DrugDomain annotations

46.0% of members

with a DrugBank compound

23.0% 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.

Proteins with classified ligands

Superclasses bound (of 23)

8.3

Superclasses per 20 proteins

broader than 64% 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	Ratio	Significance
Homogeneous metal compounds	24	11.6	2.07×	q < 0.0001
Homogeneous non-metal compounds	4	5.1	0.79×	q = 0.86
Nucleosides, nucleotides, and analogues	5	6.5	0.76×	q = 0.72
Organoheterocyclic compounds	9	3.6	2.47×	not tested
Organosulfur compounds	1	0.5	2.05×	not tested
Organic nitrogen compounds	1	0.8	1.32×	not tested
Organic oxygen compounds	5	4.7	1.06×	not tested
Benzenoids	1	1.7	0.58×	not tested
Organic acids and derivatives	1	3.7	0.27×	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
DB06185	IMH	Forodesine	14
DB03709	BCN	Bicine	8
DB04335	NOS	Inosine	6
DB04546	AD3	3-Deazaadenosine	5
DB00173	ADE	Adenine	4
DB06408	R1Y	Taribavirin	3
DB04237	TAM	Tris(Hydroxyethyl)Aminomethane	2
DB11676	UA2	Galidesivir	2
DB02059	AR6	Adenosine-5-Diphosphoribose	1
DB03345	BME	Mercaptoethanol	1

Most frequently bound compounds

PDB ligand	Name	Domains in contact
CAmetal	CALCIUM ION	177
NImetal	NICKEL (II) ION	15
IMH	1,4-DIDEOXY-4-AZA-1-(S)-(9-DEAZAHYPOXANTHIN-9-YL)-D-RIBITOL	14
RIB	alpha-D-ribofuranose	13
BCN	BICINE	8
DNB	(2S,3S,4R,5R)-2-(3,4-diaminophenyl)-5-(hydroxymethyl)pyrrolidine-3,4-diol	8
CL	CHLORIDE ION	7
MGmetal	MAGNESIUM ION	7
NOS	INOSINE	6
AD3	3-DEAZA-ADENOSINE	5
MBY	(2R,3R,4S)-2-(hydroxymethyl)-1-[(4-hydroxythieno[3,2-d]pyrimidin-7-yl)methyl]pyrrolidine-3,4-diol	5
ADE	ADENINE	4
PIR	2-(4-AMINO-PHENYL)-5-HYDROXYMETHYL-PYRROLIDINE-3,4-DIOL	4
R2O	N-(4-fluorophenyl)-4,5-dihydro-1H-imidazol-2-amine	4
R1Y	1-beta-D-ribofuranosyl-1H-1,2,4-triazole-3-carboximidamide	3
38T	5-methyluridine	2
IMQ	(2R,3R,4S)-2-(hydroxymethyl)-1-(quinolin-8-ylmethyl)pyrrolidine-3,4-diol	2
JMQ	7-(((2R,3R,4S)-3,4-dihydroxy-2-(hydroxymethyl)pyrrolidin-1-yl)methyl)-3H-pyrrolo[3,2-d]pyrimidin-4(5H)-one	2
Kmetal	POTASSIUM ION	2
NAmetal	SODIUM ION	2