X-group (possible homology)

3156 Cupredoxin-like

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Ligands and drugs

6,832

Member domains

3,760

with ligand contacts (≤ 4 Å)

55.0% of members

3,295

with DrugDomain annotations

48.2% of members

1,650

with a DrugBank compound

24.2% 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.

183

Proteins with classified ligands

Superclasses bound (of 23)

7.4

Superclasses per 20 proteins

narrower than 55% 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	176	88.6	1.99×	q < 0.0001
Homogeneous non-metal compounds	64	38.8	1.65×	q < 0.0001
Organic oxygen compounds	51	35.9	1.42×	q = 0.01
Organoheterocyclic compounds	16	27.8	0.58×	q = 0.02
Benzenoids	7	13.2	0.53×	q = 0.13
Organic nitrogen compounds	3	5.8	0.52×	q = 0.47
Lipids and lipid-like molecules	10	20.1	0.50×	q = 0.02
Organic acids and derivatives	7	27.9	0.25×	q < 0.0001
Nucleosides, nucleotides, and analogues	0	49.9	0	q < 0.0001
Mixed metal/non-metal compounds	13	3.8	3.43×	not tested
Organosulfur compounds	3	3.7	0.81×	not tested
Hydrocarbons	1	1.3	0.79×	not tested
Phenylpropanoids and polyketides	2	3.8	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	250
DB09140	OXY	Oxygen	243
DB12529	NO2	Nitrite	207
DB14522	OH	Hydroxide ion	78
DB02676	B3P	2-[3-(2-Hydroxy-1,1-Dihydroxymethyl-Ethylamino)-Propylamino]-2-Hydroxymethyl-Propane-1,3-Diol	40
DB03151	CUZ	mu4-sulfido-quadro-tetracopper	30
DB00145	GLY	Glycine	19
DB04100	REP	Tricarbonyl(1,10-phenanthroline)rhenium(1+)	16
DB11326	BO3	Boric acid	15
DB00139	SIN	Succinic acid	13
DB02736	ACM	Acetamide	12
DB11091	PEO	Hydrogen peroxide	10
DB03317	HEC	Ferroheme C	9
DB02163	XYD	2,5-Xylidine	8
DB06690	N2O	Nitrous oxide	6
DB09130	—	—	6
DB01373	—	—	5
DB01592	—	—	5
DB01593	—	—	5
DB12965	—	—	5

Most frequently bound compounds

PDB ligand	Name	Domains in contact
CUmetal	COPPER (II) ION	2,711
CUA	DINUCLEAR COPPER ION	331
OXY	OXYGEN MOLECULE	285
MGmetal	MAGNESIUM ION	275
NO2	NITRITE ION	262
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	223
CL	CHLORIDE ION	179
CU1metal	COPPER (I) ION	147
ZNmetal	ZINC ION	119
NAmetal	SODIUM ION	115
CAmetal	CALCIUM ION	92
C2O	CU-O-CU LINKAGE	90
OH	HYDROXIDE ION	80
O	OXYGEN ATOM	74
MRD	(4R)-2-METHYLPENTANE-2,4-DIOL	67
NO	NITRIC OXIDE	65
PER	PEROXIDE ION	42
B3P	2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL	40
CDmetal	CADMIUM ION	33
GLY	GLYCINE	30