X-group (possible homology)

5 beta-propeller-like

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Ligands and drugs

31,251

Member domains

5,824

with ligand contacts (≤ 4 Å)

18.6% of members

4,998

with DrugDomain annotations

16.0% of members

3,633

with a DrugBank compound

11.6% 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.

564

Proteins with classified ligands

Superclasses bound (of 23)

7.8

Superclasses per 20 proteins

broader 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	279	110.7	2.52×	q < 0.0001
Homogeneous metal compounds	341	273.0	1.25×	q < 0.0001
Homogeneous non-metal compounds	138	119.7	1.15×	q = 0.10
Organoheterocyclic compounds	92	85.6	1.07×	q = 0.52
Phenylpropanoids and polyketides	12	11.6	1.04×	q = 0.92
Organic acids and derivatives	88	86.0	1.02×	q = 0.87
Organic nitrogen compounds	18	17.7	1.01×	q = 0.94
Benzenoids	37	40.7	0.91×	q = 0.70
Organosulfur compounds	6	11.4	0.52×	q = 0.18
Mixed metal/non-metal compounds	6	11.7	0.51×	q = 0.15
Lipids and lipid-like molecules	17	61.9	0.28×	q < 0.0001
Nucleosides, nucleotides, and analogues	6	153.7	0.04×	q < 0.0001
Miscellaneous inorganic compounds	2	0.4	4.82×	not tested
Hydrocarbon derivatives	1	0.5	2.09×	not tested
Alkaloids and derivatives	2	1.9	1.05×	not tested
Hydrocarbons	1	3.9	0.26×	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	1,220
DB02600	G39	Oseltamivir acid	105
DB03205	PQQ	Pyrroloquinoline Quinone	97
DB03991	DAN	2-deoxy-2,3-dehydro-N-acetylneuraminic acid	75
DB03469	DHE	Heme D	56
DB03879	MFU	alpha-L-methyl-fucose	56
DB00558	ZMR	Zanamivir	54
DB04473	FUC	alpha-L-fucose	51
DB02676	B3P	2-[3-(2-Hydroxy-1,1-Dihydroxymethyl-Ethylamino)-Propylamino]-2-Hydroxymethyl-Propane-1,3-Diol	48
DB03721	SIA	N-acetyl-alpha-neuraminic acid	48
DB02561	BDF	Beta-D-Fructopyranose	38
DB03740	NDG	N-acetyl-alpha-D-glucosamine	36
DB03151	CUZ	mu4-sulfido-quadro-tetracopper	30
DB06614	BCZ	Peramivir	27
DB03796	PLM	Palmitic Acid	21
DB00786	—	Marimastat	20
DB03283	FUL	beta-L-fucose	20
DB03317	HEC	Ferroheme C	19
DB00145	GLY	Glycine	18
DB01979	MMA	Methyl alpha-D-mannoside	13

Most frequently bound compounds

PDB ligand	Name	Domains in contact
CAmetal	CALCIUM ION	1,500
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	1,189
CL	CHLORIDE ION	524
NAmetal	SODIUM ION	433
MGmetal	MAGNESIUM ION	179
ZNmetal	ZINC ION	145
FE2metal	FE (II) ION	135
G39	(3R,4R,5S)-4-(acetylamino)-5-amino-3-(pentan-3-yloxy)cyclohex-1-ene-1-carboxylic acid	105
UNX	UNKNOWN ATOM OR ION	105
CUmetal	COPPER (II) ION	101
Kmetal	POTASSIUM ION	101
PQQ	PYRROLOQUINOLINE QUINONE	96
BDF	beta-D-fructopyranose	77
DAN	2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID	76
OHX	osmium (III) hexammine	70
MFU	methyl alpha-L-fucopyranoside	66
MAN	alpha-D-mannopyranose	61
NDG	2-acetamido-2-deoxy-alpha-D-glucopyranose	59
DHE	HEME D	56
B3P	2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL	54