X-group (possible homology)

6 beta-Trefoil

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Ligands and drugs

4,440

Member domains

1,211

with ligand contacts (≤ 4 Å)

27.3% of members

1,004

with DrugDomain annotations

22.6% of members

753

with a DrugBank compound

17.0% 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)

7.5

Superclasses per 20 proteins

narrower than 52% 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	68	19.4	3.50×	q < 0.0001
Homogeneous non-metal compounds	30	21.0	1.43×	q = 0.06
Benzenoids	9	7.1	1.26×	q = 0.52
Organic acids and derivatives	9	15.1	0.60×	q = 0.14
Organoheterocyclic compounds	7	15.0	0.47×	q = 0.04
Homogeneous metal compounds	22	47.9	0.46×	q < 0.0001
Lipids and lipid-like molecules	1	10.9	0.09×	q = 7.7e-4
Nucleosides, nucleotides, and analogues	1	27.0	0.04×	q < 0.0001
Organic nitrogen compounds	4	3.1	1.28×	not tested
Organosulfur compounds	2	2.0	1.00×	not tested
Phenylpropanoids and polyketides	2	2.0	0.98×	not tested
Mixed metal/non-metal compounds	1	2.1	0.49×	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	73
DB03401	I3P	1D-myo-inositol 1,4,5-trisphosphate	21
DB03975	MBO	Mercuribenzoic Acid	16
DB03567	A2G	alpha-N-Acetyl-D-galactosamine	14
DB04265	SLB	N-acetyl-beta-neuraminic acid	10
DB04506	CHL	Chlorophyll B	9
DB02133	CLA	Chlorophyll A	8
DB03721	SIA	N-acetyl-alpha-neuraminic acid	8
DB01862	IPT	Isopropyl beta-D-thiogalactopyranoside	7
DB02379	BGC	Beta-D-Glucose	7
DB04447	DTT	1,4-Dithiothreitol	7
DB02100	AMG	Methyl alpha-galactoside	5
DB00133	SER	Serine	4
DB02042	1PG	2-(2-{2-[2-(2-Methoxy-Ethoxy)-Ethoxy]-Ethoxy}-Ethoxy)-Ethanol	4
DB00686	—	—	3
DB03142	AHR	Alpha-L-Arabinose	3
DB03345	BME	Mercaptoethanol	3
DB08238	N2M	5-aminonaphthalene-2-sulfonic acid	3
DB13529	DBX	Dobesilic acid	3
DB00145	GLY	Glycine	2

Most frequently bound compounds

PDB ligand	Name	Domains in contact
CL	CHLORIDE ION	87
I3P	D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE	74
CAmetal	CALCIUM ION	66
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	58
GAL	beta-D-galactopyranose	46
NGA	2-acetamido-2-deoxy-beta-D-galactopyranose	36
MGmetal	MAGNESIUM ION	35
NAmetal	SODIUM ION	32
A2G	2-acetamido-2-deoxy-alpha-D-galactopyranose	29
BR	BROMIDE ION	20
MBO	MERCURIBENZOIC ACID	16
GLA	alpha-D-galactopyranose	13
C7V	4-methyl-N-(1-{[4-(trifluoromethyl)phenyl]methyl}-1H-indazol-3-yl)-1,2-oxazole-5-carboxamide	12
HGmetal	MERCURY (II) ION	12
NImetal	NICKEL (II) ION	11
XYP	beta-D-xylopyranose	11
ZNmetal	ZINC ION	11
SLB	N-acetyl-beta-neuraminic acid	10
AMG	methyl alpha-D-galactopyranoside	9
CHL	CHLOROPHYLL B	9