X-group (possible homology)

146 Di-copper centre-containing domain

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Ligands and drugs

861

Member domains

399

with ligand contacts (≤ 4 Å)

46.3% of members

279

with DrugDomain annotations

32.4% of members

155

with a DrugBank compound

18.0% 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)

8.5

Superclasses per 20 proteins

broader than 66% 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 non-metal compounds	15	7.6	1.96×	q = 0.01
Homogeneous metal compounds	32	17.4	1.84×	q < 0.0001
Organoheterocyclic compounds	5	5.5	0.92×	q = 1.00
Organic acids and derivatives	5	5.5	0.91×	q = 1.00
Organic oxygen compounds	4	7.1	0.57×	q = 0.36
Nucleosides, nucleotides, and analogues	0	9.8	0	q < 0.0001
Hydrocarbon derivatives	2	0.0	66×	not tested
Mixed metal/non-metal compounds	3	0.8	4.02×	not tested
Organosulfur compounds	2	0.7	2.74×	not tested
Benzenoids	6	2.6	2.31×	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	47
DB00135	TYR	Tyrosine	12
DB01759	KOJ	Kojic acid	12
DB01055	MMS	Mimosine	9
DB03694	URS	N-phenylthiourea	8
DB11085	RCO	Resorcinol	7
DB09526	HQE	Hydroquinone	5
DB01235	DAH	Levodopa	3
DB09140	OXY	Oxygen	3
DB11091	PEO	Hydrogen peroxide	3
DB00145	GLY	Glycine	2
DB16855	YRL	Tyrosol	2
DB00157	—	NADH	1
DB00548	—	Azelaic acid	1
DB00600	—	—	1
DB03967	SDS	Dodecyl sulfate	1
DB11217	—	Arbutin	1
DB11254	—	—	1

Most frequently bound compounds

PDB ligand	Name	Domains in contact
CUmetal	COPPER (II) ION	224
CUO	CU2-O2 CLUSTER	92
ZNmetal	ZINC ION	61
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	42
O	OXYGEN ATOM	18
PER	PEROXIDE ION	16
CL	CHLORIDE ION	15
NAmetal	SODIUM ION	15
MAN	alpha-D-mannopyranose	14
0TR	2-HYDROXYCYCLOHEPTA-2,4,6-TRIEN-1-ONE	12
KOJ	5-HYDROXY-2-(HYDROXYMETHYL)-4H-PYRAN-4-ONE	12
TYR	TYROSINE	12
MMS	MIMOSINE	8
URS	N-PHENYLTHIOUREA	8
MGmetal	MAGNESIUM ION	7
RCO	RESORCINOL	7
C2O	CU-O-CU LINKAGE	6
HOmetal	HOLMIUM ATOM	6
TEW	6-tungstotellurate(VI)	6
TRP	TRYPTOPHAN	6