X-group (possible homology)

242 Homing endonucleases-like

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Ligands and drugs

2,628

Member domains

409

with ligand contacts (≤ 4 Å)

15.6% of members

317

with DrugDomain annotations

12.1% of members

with a DrugBank compound

2.2% 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.

Proteins with classified ligands

Superclasses bound (of 23)

2.9

Superclasses per 20 proteins

narrower than 96% 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	25	14.0	1.78×	q = 1.4e-4
Homogeneous non-metal compounds	5	6.2	0.81×	q = 0.88
Organic oxygen compounds	2	5.7	0.35×	q = 0.15
Nucleosides, nucleotides, and analogues	0	7.9	0	q = 5.5e-4

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
DB04349	PGO	(S)-propane-1,2-diol	10
DB02806	MXE	2-Methoxyethanol	3

Most frequently bound compounds

PDB ligand	Name	Domains in contact
CAmetal	CALCIUM ION	198
MNmetal	MANGANESE (II) ION	96
MGmetal	MAGNESIUM ION	67
CL	CHLORIDE ION	22
NAmetal	SODIUM ION	16
PGO	S-1,2-PROPANEDIOL	12
ZNmetal	ZINC ION	10
MXE	2-METHOXYETHANOL	3
AUmetal	GOLD ION	2
Kmetal	POTASSIUM ION	2
NImetal	NICKEL (II) ION	2
A23	ADENOSINE-5'-PHOSPHATE-2',3'-CYCLIC PHOSPHATE	1
CDmetal	CADMIUM ION	1
PG0	2-(2-METHOXYETHOXY)ETHANOL	1