X-group (possible homology)

2010 EDD domain

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Ligands and drugs

379

Member domains

with ligand contacts (≤ 4 Å)

25.1% of members

with DrugDomain annotations

25.3% of members

with a DrugBank compound

20.6% 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.

Proteins with classified ligands

Superclasses bound (of 23)

4.9

Superclasses per 20 proteins

narrower than 84% 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	5	12.1	0.41×	q = 9.3e-3
Homogeneous non-metal compounds	2	5.3	0.38×	q = 0.20
Nucleosides, nucleotides, and analogues	2	6.8	0.29×	q = 0.06
Lipids and lipid-like molecules	18	2.7	6.56×	not tested
Organic oxygen compounds	6	4.9	1.22×	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
DB03796	PLM	Palmitic Acid	22
DB08231	MYR	Myristic acid	7
DB01775	2HA	Dihydroxyacetone	6
DB04801	VCA	cis-Vaccenic acid	4
DB16833	ADP	Adenosine disphosphate	3
DB02263	G3H	D-glyceraldehyde 3-phosphate	2
DB02580	PG6	Pentaglyme	2
DB03193	STE	Stearic acid	2
DB03756	HXA	Doconexent	2
DB14104	EIC	Linoleic acid	2
DB04224	ELA	Oleic Acid	1

Most frequently bound compounds

PDB ligand	Name	Domains in contact
PLM	PALMITIC ACID	22
NAmetal	SODIUM ION	8
MYR	MYRISTIC ACID	7
2HA	Dihydroxyacetone	6
CAmetal	CALCIUM ION	6
OLA	OLEIC ACID	4
VCA	VACCENIC ACID	4
ADP	ADENOSINE-5'-DIPHOSPHATE	3
ZNmetal	ZINC ION	3
15P	POLYETHYLENE GLYCOL (N=34)	2
BMJ	(12R)-12-methyltetradecanoic acid	2
BNV	(12S)-12-methyltetradecanoic acid	2
D0G	(14S)-14-methylhexadecanoic acid	2
EIC	LINOLEIC ACID	2
G3H	GLYCERALDEHYDE-3-PHOSPHATE	2
HXA	DOCOSA-4,7,10,13,16,19-HEXAENOIC ACID	2
PG6	1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE	2
STE	STEARIC ACID	2
BR	BROMIDE ION	1
CL	CHLORIDE ION	1