X-group (possible homology)

5090 Viral glycoprotein, central and dimerisation domains-like

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Ligands and drugs

1,288

Member domains

325

with ligand contacts (≤ 4 Å)

25.2% of members

263

with DrugDomain annotations

20.4% of members

248

with a DrugBank compound

19.3% 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)

5.0

Superclasses per 20 proteins

narrower than 82% 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	48	10.0	4.79×	q < 0.0001
Lipids and lipid-like molecules	4	5.6	0.71×	q = 0.73
Homogeneous non-metal compounds	6	10.8	0.55×	q = 0.17
Homogeneous metal compounds	9	24.7	0.36×	q < 0.0001
Organoheterocyclic compounds	1	7.7	0.13×	q = 0.01
Nucleosides, nucleotides, and analogues	0	13.9	0	q < 0.0001
Organic acids and derivatives	0	7.8	0	q = 8.7e-4
Mixed metal/non-metal compounds	1	1.1	0.95×	not tested
Organic nitrogen compounds	1	1.6	0.62×	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	218
DB02306	CPL	Palmitoyl-Linoleoyl Phosphatidylcholine	2
DB03350	NCO	Cobalt hexammine ion	1
DB03740	NDG	N-acetyl-alpha-D-glucosamine	1

Most frequently bound compounds

PDB ligand	Name	Domains in contact
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	279
CAmetal	CALCIUM ION	16
NAmetal	SODIUM ION	13
CL	CHLORIDE ION	9
BR	BROMIDE ION	6
HOmetal	HOLMIUM ATOM	6
NGA	2-acetamido-2-deoxy-beta-D-galactopyranose	6
CDmetal	CADMIUM ION	5
Kmetal	POTASSIUM ION	5
43Y	[(2R)-3-[oxidanyl-[2-(trimethyl-$l^{4}-azanyl)ethoxy]phosphoryl]oxy-2-propanoyloxy-propyl] propanoate	3
CPL	1-PALMITOYL-2-LINOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE	3
6OU	[(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate	1
CCN	ACETONITRILE	1
KH2	3-(1-methylpiperidinium-1-yl)propane-1-sulfonate	1
NCO	COBALT HEXAMMINE(III)	1
NDG	2-acetamido-2-deoxy-alpha-D-glucopyranose	1
OSmetal	OSMIUM ION	1
ZNmetal	ZINC ION	1