X-group (possible homology)

4016 alpha-helical domain in type II DNA topoisomerase

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Ligands and drugs

611

Member domains

with ligand contacts (≤ 4 Å)

11.5% of members

with DrugDomain annotations

8.2% of members

with a DrugBank compound

5.9% 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
Lignans, neolignans and related compounds	1	0.0	272×	not tested
Homogeneous non-metal compounds	4	1.1	3.77×	not tested
Organoheterocyclic compounds	2	0.8	2.64×	not tested
Organic acids and derivatives	1	0.8	1.31×	not tested
Homogeneous metal compounds	3	2.4	1.24×	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
DB00145	GLY	Glycine	1
DB00773	EVP	Etoposide	1

Most frequently bound compounds

PDB ligand	Name	Domains in contact
CL	CHLORIDE ION	17
MNmetal	MANGANESE (II) ION	10
94H	~{N}-[(1~{R})-2-azanyl-1-phenyl-ethyl]-4-(1~{H}-pyrrolo[2,3-b]pyridin-3-yl)thiophene-2-carboxamide	4
NAmetal	SODIUM ION	4
MGmetal	MAGNESIUM ION	3
94K	~{N}-[(1~{R})-2-azanyl-1-phenyl-ethyl]-5-(2-chlorophenyl)-2-methyl-thiophene-3-carboxamide	2
9JN	~{N}-[(1~{S})-2-azanyl-1-phenyl-ethyl]-4-(1~{H}-pyrrolo[2,3-b]pyridin-3-yl)thiophene-2-carboxamide	2
MLA	MALONIC ACID	2
CPF	1-CYCLOPROPYL-6-FLUORO-4-OXO-7-PIPERAZIN-1-YL-1,4-DIHYDROQUINOLINE-3-CARBOXYLIC ACID	1
GLY	GLYCINE	1