X-group (possible homology)

330 dsRBD-like

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Ligands and drugs

9,581

Member domains

854

with ligand contacts (≤ 4 Å)

8.9% of members

601

with DrugDomain annotations

6.3% of members

216

with a DrugBank compound

2.3% 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.

Proteins with classified ligands

Superclasses bound (of 23)

6.6

Superclasses per 20 proteins

narrower than 67% 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	36	26.6	1.35×	q = 0.03
Organic acids and derivatives	11	8.4	1.31×	q = 0.42
Organoheterocyclic compounds	7	8.4	0.84×	q = 0.78
Homogeneous non-metal compounds	8	11.7	0.69×	q = 0.33
Nucleosides, nucleotides, and analogues	6	15.0	0.40×	q = 0.01
Lipids and lipid-like molecules	1	6.0	0.17×	q = 0.05
Organic oxygen compounds	0	10.8	0	q < 0.0001
Organosulfur compounds	2	1.1	1.79×	not tested
Phenylpropanoids and polyketides	1	1.1	0.89×	not tested
Mixed metal/non-metal compounds	1	1.1	0.88×	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
DB00131	AMP	Adenosine phosphate	27
DB16833	ADP	Adenosine disphosphate	27
DB04517	DPM	Dipyrromethane Cofactor	21
DB03909	ACP	Adenosine-5'-[Beta, Gamma-Methylene]Triphosphate	18
DB00171	ATP	ATP	15
DB02596	APC	alpha,beta-Methyleneadenosine 5'-triphosphate	15
DB00919	SCM	Spectinomycin	13
DB00161	VAL	Valine	12
DB03940	OXM	Oxamic Acid	8
DB02181	DGT	2'-Deoxyguanosine-5'-Triphosphate	6
DB04137	GTP	Guanosine-5'-Triphosphate	6
DB00149	LEU	Leucine	4
DB00167	ILE	Isoleucine	4
DB00759	TAC	Tetracycline	2
DB03345	BME	Mercaptoethanol	2
DB00328	—	Indomethacin	1
DB07995	—	H-89	1
DB09130	—	—	1
DB12010	—	Fostamatinib	1

Most frequently bound compounds

PDB ligand	Name	Domains in contact
MGmetal	MAGNESIUM ION	642
AMP	ADENOSINE MONOPHOSPHATE	27
OHX	osmium (III) hexammine	27
Kmetal	POTASSIUM ION	25
ADP	ADENOSINE-5'-DIPHOSPHATE	22
DPM	3-[5-{[3-(2-carboxyethyl)-4-(carboxymethyl)-5-methyl-1H-pyrrol-2-yl]methyl}-4-(carboxymethyl)-1H-pyrrol-3-yl]propanoic acid	21
CL	CHLORIDE ION	20
ACP	PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER	18
SCM	SPECTINOMYCIN	16
APC	DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER	15
ATP	ADENOSINE-5'-TRIPHOSPHATE	15
7J8	3-[4-(2-hydroxy-2-oxoethyl)-5-[[4-(2-hydroxy-2-oxoethyl)-5-[[4-(2-hydroxy-2-oxoethyl)-5-[[4-(2-hydroxy-2-oxoethyl)-3-(3-hydroxy-3-oxopropyl)-5-methyl-1~{H}-pyrrol-2-yl]methyl]-3-(3-hydroxy-3-oxopropyl)-1~{H}-pyrrol-2-yl]methyl]-3-(3-hydroxy-3-oxopropyl)-1~{H}-pyrrol-2-yl]methyl]-1~{H}-pyrrol-3-yl]propanoic acid	8
CAmetal	CALCIUM ION	8
OXM	OXAMIC ACID	8
ANP	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER	6
DGT	2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE	6
GTP	GUANOSINE-5'-TRIPHOSPHATE	6
UNX	UNKNOWN ATOM OR ION	6
ZNmetal	ZINC ION	5
ILE	ISOLEUCINE	4