X-group (possible homology)

12 Glycosyl hydrolase domain-like

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Ligands and drugs

10,047

Member domains

2,548

with ligand contacts (≤ 4 Å)

25.4% of members

2,252

with DrugDomain annotations

22.4% of members

1,393

with a DrugBank compound

13.9% 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.

192

Proteins with classified ligands

Superclasses bound (of 23)

6.5

Superclasses per 20 proteins

narrower than 68% 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
Organic oxygen compounds	104	37.7	2.76×	q < 0.0001
Homogeneous metal compounds	94	92.9	1.01×	q = 0.93
Organic nitrogen compounds	6	6.0	0.99×	q = 1.00
Benzenoids	13	13.8	0.94×	q = 1.00
Homogeneous non-metal compounds	37	40.7	0.91×	q = 0.67
Organoheterocyclic compounds	24	29.1	0.82×	q = 0.44
Organic acids and derivatives	16	29.3	0.55×	q = 0.01
Lipids and lipid-like molecules	2	21.1	0.10×	q < 0.0001
Nucleosides, nucleotides, and analogues	1	52.3	0.02×	q < 0.0001
Alkaloids and derivatives	1	0.7	1.55×	not tested
Organosulfur compounds	1	3.9	0.26×	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	304
DB02379	BGC	Beta-D-Glucose	56
DB01862	IPT	Isopropyl beta-D-thiogalactopyranoside	33
DB01885	149	D-Galctopyranosyl-1-On	32
DB02178	HY1	Phenylacetaldehyde	24
DB11091	PEO	Hydrogen peroxide	22
DB02228	2FG	2-deoxy-2-fluoro-β-D-galactose	20
DB09459	TLA	L-tartaric acid	15
DB02034	SWA	Tridolgosir	14
DB03434	MPO	3-(N-morpholino)propanesulfonic acid	13
DB04382	2DG	2-Deoxy-alpha-D-galactopyranose	13
DB05018	DGJ	Migalastat	13
DB00139	SIN	Succinic acid	10
DB00284	—	—	8
DB02294	GTZ	(5R,6S,7S,8S)-5-hydroxymethyl-6,7,8-trihydroxy-tetrazolo[1,5-A]piperidine	8
DB04878	VOG	Voglibose	7
DB00491	—	Miglitol	6
DB02464	ABN	Benzylamine	6
DB02742	KIF	Kifunensine	6
DB04807	XTG	4-NITROPHENYL-(6-S-ALPHA-D-XYLOPYRANOSYL)-BETA-D-GLUCOPYRANOSIDE	6

Most frequently bound compounds

PDB ligand	Name	Domains in contact
NAmetal	SODIUM ION	496
CUmetal	COPPER (II) ION	301
CAmetal	CALCIUM ION	257
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	225
CL	CHLORIDE ION	109
MGmetal	MAGNESIUM ION	100
IPT	1-methylethyl 1-thio-beta-D-galactopyranoside	45
BGC	beta-D-glucopyranose	44
GAL	beta-D-galactopyranose	29
ZNmetal	ZINC ION	29
HY1	PHENYLACETALDEHYDE	24
NImetal	NICKEL (II) ION	22
P6G	HEXAETHYLENE GLYCOL	22
PEO	HYDROGEN PEROXIDE	22
GLC	alpha-D-glucopyranose	19
IOD	IODIDE ION	19
Kmetal	POTASSIUM ION	18
149	D-galactonolactone	17
MNmetal	MANGANESE (II) ION	16
MVL	(5R,6R,7S,8R)-5-(HYDROXYMETHYL)-5,6,7,8-TETRAHYDROIMIDAZO[1,2-A]PYRIDINE-6,7,8-TRIOL	16