X-group (possible homology)

2487 The "swivelling" beta/beta/alpha domains

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Ligands and drugs

8,709

Member domains

695

with ligand contacts (≤ 4 Å)

8.0% of members

437

with DrugDomain annotations

5.0% of members

272

with a DrugBank compound

3.1% 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)

8.6

Superclasses per 20 proteins

broader than 71% 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 acids and derivatives	15	9.2	1.64×	q = 0.07
Organic oxygen compounds	13	11.8	1.10×	q = 0.70
Homogeneous metal compounds	32	29.0	1.10×	q = 0.60
Homogeneous non-metal compounds	13	12.7	1.02×	q = 0.92
Lipids and lipid-like molecules	4	6.6	0.61×	q = 0.48
Nucleosides, nucleotides, and analogues	7	16.4	0.43×	q = 0.01
Organoheterocyclic compounds	3	9.1	0.33×	q = 0.05
Phenylpropanoids and polyketides	2	1.2	1.63×	not tested
Mixed metal/non-metal compounds	2	1.2	1.61×	not tested
Benzenoids	3	4.3	0.69×	not tested
Organic nitrogen compounds	1	1.9	0.53×	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	120
DB00131	AMP	Adenosine phosphate	13
DB00139	SIN	Succinic acid	12
DB00130	GLN	L-Glutamine	8
DB00142	GLU	Glutamic acid	5
DB09459	TLA	L-tartaric acid	5
DB00129	ORN	Ornithine	4
DB00676	BZM	Benzyl benzoate	4
DB02897	UVW	Acetylphosphate	4
DB03376	A5A	5'-O-(N-(Alanyl)sulfamoyl)adenosine	4
DB04351	TRA	Aconitate Ion	4
DB02999	QUS	Quisqualic acid	3
DB04343	GLV	Glyoxylic acid	3
DB04562	TRC	Tricarballylic acid	3
DB09157	CO2	Carbon dioxide	3
DB01819	PEP	Phosphoenolpyruvate	2
DB02175	MLA	Malonic acid	2
DB02606	SBT	2-Butanol	2
DB02916	LMS	[(2r,3s,4r,5r)-5-(6-Amino-9h-Purin-9-Yl)-3,4-Dihydroxytetrahydro-2-Furanyl]Methyl Sulfamate	2
DB03964	ATH	4-Hydroxy-Aconitate Ion	2

Most frequently bound compounds

PDB ligand	Name	Domains in contact
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	154
CAmetal	CALCIUM ION	137
MGmetal	MAGNESIUM ION	108
ATP	ADENOSINE-5'-TRIPHOSPHATE	77
CL	CHLORIDE ION	48
Kmetal	POTASSIUM ION	40
MNmetal	MANGANESE (II) ION	40
SF4	IRON/SULFUR CLUSTER	36
ADP	ADENOSINE-5'-DIPHOSPHATE	33
ZNmetal	ZINC ION	33
ANP	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER	28
TLmetal	THALLIUM (I) ION	28
LMR	(2S)-2-hydroxybutanedioic acid	19
NAmetal	SODIUM ION	17
AF3	ALUMINUM FLUORIDE	16
23J	oxo(2-sulfanylphenyl)acetic acid	12
SIN	SUCCINIC ACID	12
AMP	ADENOSINE MONOPHOSPHATE	11
DSZ	5'-O-(L-alpha-aspartylsulfamoyl)adenosine	8
GLN	GLUTAMINE	8