X-group (possible homology)

207 Single-stranded right-handed beta-helix

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Ligands and drugs

18,573

Member domains

2,041

with ligand contacts (≤ 4 Å)

11.0% of members

1,724

with DrugDomain annotations

9.3% of members

1,356

with a DrugBank compound

7.3% 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.

236

Proteins with classified ligands

Superclasses bound (of 23)

6.1

Superclasses per 20 proteins

narrower than 73% 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	123	46.3	2.65×	q < 0.0001
Homogeneous non-metal compounds	56	50.1	1.12×	q = 0.42
Homogeneous metal compounds	109	114.2	0.95×	q = 0.59
Benzenoids	8	17.0	0.47×	q = 0.04
Organic nitrogen compounds	3	7.4	0.40×	q = 0.18
Lipids and lipid-like molecules	10	25.9	0.39×	q = 9.3e-4
Organic acids and derivatives	7	36.0	0.19×	q < 0.0001
Organoheterocyclic compounds	5	35.8	0.14×	q < 0.0001
Nucleosides, nucleotides, and analogues	5	64.3	0.08×	q < 0.0001
Miscellaneous inorganic compounds	1	0.2	5.76×	not tested
Organometallic compounds	1	0.3	3.02×	not tested
Organosulfur compounds	2	4.8	0.42×	not tested
Mixed metal/non-metal compounds	2	4.9	0.41×	not tested
Phenylpropanoids and polyketides	1	4.8	0.21×	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	845
DB02745	URI	Uridine	23
DB06530	RX8	Resiquimod	16
DB03511	ADA	alpha-D-galacturonic acid	14
DB03652	GTR	beta-D-Galactopyranuronic acid	12
DB02379	BGC	Beta-D-Glucose	10
DB14981	IHP	Phytic acid	9
DB12010	—	Fostamatinib	7
DB00724	6T0	Imiquimod	6
DB02857	GMP	Guanosine	6
DB08231	MYR	Myristic acid	6
DB15035	—	—	6
DB02082	GNP	Phosphoaminophosphonic acid guanylate ester	5
DB04315	GDP	Guanosine-5'-Diphosphate	5
DB03389	XYS	alpha-D-Xylopyranose	4
DB04564	LGC	Gluconolactone	4
DB05475	—	—	4
DB05944	—	—	4
DB06021	—	—	4
DB08916	—	Afatinib	4

Most frequently bound compounds

PDB ligand	Name	Domains in contact
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	1,004
CAmetal	CALCIUM ION	258
CL	CHLORIDE ION	147
NAmetal	SODIUM ION	88
MGmetal	MAGNESIUM ION	75
ZNmetal	ZINC ION	67
IHP	INOSITOL HEXAKISPHOSPHATE	27
URI	URIDINE	25
IDQ	1-[[4-(aminomethyl)phenyl]methyl]-2-butyl-imidazo[4,5-c]quinolin-4-amine	21
MAN	alpha-D-mannopyranose	18
RX8	1-[4-amino-2-(ethoxymethyl)-1H-imidazo[4,5-c]quinolin-1-yl]-2-methylpropan-2-ol	17
NImetal	NICKEL (II) ION	16
OGK	(1S,2S)-2-ethyl-1-({[(3aS,4S,6R,7aS)-6-ethyl-1-oxooctahydro-1H-inden-4-yl]carbonyl}amino)cyclopropanecarboxylic acid	16
UCG	3'-O-[(R)-{[(2R,3aR,4R,6R,6aR)-6-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-2-hydroxy-2-oxidotetrahydrofuro[3,4-d][1,3,2]dioxaphosphol-4-yl]methoxy}(hydroxy)phosphoryl]uridine 5'-(dihydrogen phosphate)	16
BLD	Brassinolide	15
Kmetal	POTASSIUM ION	13
9F3	(2R,3'S,4'S,4aR,5'R,6R,7R,7aS)-4a,5',6-tris(hydroxymethyl)spiro[3,6,7,7a-tetrahydrofuro[2,3-b][1,4]dioxine-2,2'-oxolane]-3',4',7-triol	12
ADA	alpha-D-galactopyranuronic acid	12
GTR	beta-D-galactopyranuronic acid	11
MRD	(4R)-2-METHYLPENTANE-2,4-DIOL	11