X-group (possible homology)

3688 N-terminal subdomain in UbiD middle domain

Open in classification tree →

Ligands and drugs

400

Member domains

with ligand contacts (≤ 4 Å)

8.3% of members

with DrugDomain annotations

3.3% of members

with a DrugBank compound

1.8% 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)

—

Superclasses per 20 proteins

fewer than 20 proteins: too few to compare at equal depth

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
Benzenoids	1	0.2	4.62×	not tested
Organic oxygen compounds	1	0.6	1.70×	not tested
Homogeneous metal compounds	1	1.5	0.69×	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
DB03514	4M4	4-Vinylguaiacol	1

Most frequently bound compounds

PDB ligand	Name	Domains in contact
BYC	benzoyl coenzyme A	6
WC8	2-CN-benzoyl coenzyme A	6
NAmetal	SODIUM ION	3
Kmetal	POTASSIUM ION	2
SCN	THIOCYANATE ION	2
4M4	2-Methoxy-4-vinylphenol	1
9JE	pentane-1,5-diol	1