X-group (possible homology)

627 VPS9 domain

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Ligands and drugs

213

Member domains

with ligand contacts (≤ 4 Å)

3.8% of members

with DrugDomain annotations

3.8% of members

with a DrugBank compound

3.3% 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)

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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	0.25×observed / expected4×	Ratio	Significance
Homogeneous metal compounds	2	1.0		2.07×	not tested
Nucleosides, nucleotides, and analogues	1	0.6		1.83×	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
DB04315	GDP	Guanosine-5'-Diphosphate	5
DB02623	GNH	Aminophosphonic acid-guanylate ester	2

Most frequently bound compounds

PDB ligand	Name	Domains in contact
GDP	GUANOSINE-5'-DIPHOSPHATE	5
GNH	AMINOPHOSPHONIC ACID-GUANYLATE ESTER	2
CAmetal	CALCIUM ION	1
MGmetal	MAGNESIUM ION	1