X-group (possible homology)

378 His-Me finger endonucleases

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Ligands and drugs

1,424

Member domains

688

with ligand contacts (≤ 4 Å)

48.3% of members

373

with DrugDomain annotations

26.2% of members

158

with a DrugBank compound

11.1% 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)

4.3

Superclasses per 20 proteins

narrower than 88% 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	56	27.1	2.07×	q < 0.0001
Homogeneous non-metal compounds	15	11.9	1.26×	q = 0.40
Organic oxygen compounds	10	11.0	0.91×	q = 0.91
Organoheterocyclic compounds	1	8.5	0.12×	q = 4.9e-3
Organic acids and derivatives	1	8.5	0.12×	q = 5.0e-3
Lipids and lipid-like molecules	0	6.2	0	q = 5.0e-3
Nucleosides, nucleotides, and analogues	0	15.3	0	q < 0.0001
Organosulfur compounds	2	1.1	1.76×	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	57
DB02175	MLA	Malonic acid	3
DB04522	—	Dexfosfoserine	1
DB06408	—	Taribavirin	1

Most frequently bound compounds

PDB ligand	Name	Domains in contact
NAmetal	SODIUM ION	315
CAmetal	CALCIUM ION	309
ZNmetal	ZINC ION	242
MGmetal	MAGNESIUM ION	156
Kmetal	POTASSIUM ION	113
CL	CHLORIDE ION	54
MNmetal	MANGANESE (II) ION	30
IOD	IODIDE ION	28
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	24
SCN	THIOCYANATE ION	19
NImetal	NICKEL (II) ION	8
BR	BROMIDE ION	4
MLA	MALONIC ACID	3
CDmetal	CADMIUM ION	2
GTP	GUANOSINE-5'-TRIPHOSPHATE	2
STL	RESVERATROL	2
TLmetal	THALLIUM (I) ION	2
6ZO	(3,5-dichlorophenyl)methyl 4-[3-oxo-3-(2-oxo-2,3-dihydro-1,3-benzoxazol-6-yl)propyl]piperazine-1-carboxylate	1
BAmetal	BARIUM ION	1
PBmetal	LEAD (II) ION	1