X-group (possible homology)

2012 LigB-like

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Ligands and drugs

330

Member domains

with ligand contacts (≤ 4 Å)

22.1% of members

with DrugDomain annotations

17.3% of members

with a DrugBank compound

6.1% 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)

—

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
Benzenoids	4	0.7	6.17×	not tested
Homogeneous metal compounds	8	4.4	1.84×	not tested
Homogeneous non-metal compounds	2	1.9	1.05×	not tested
Organoheterocyclic compounds	1	1.4	0.73×	not tested
Organic acids and derivatives	1	1.4	0.73×	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
DB00143	GSH	Glutathione	8
DB03946	DHB	3,4-Dihydroxybenzoic Acid	3
DB03407	4NC	4-Nitrocatechol	2
DB14522	OH	Hydroxide ion	1

Most frequently bound compounds

PDB ligand	Name	Domains in contact
FE2metal	FE (II) ION	35
FEmetal	FE (III) ION	14
A1EG2	3-[2,3-bis(oxidanyl)phenyl]propanoic acid	10
GDE	3,4,5-trihydroxybenzoic acid	8
GSH	Glutathione	8
ZNmetal	ZINC ION	5
CU1metal	COPPER (I) ION	4
NAmetal	SODIUM ION	4
DHB	3,4-DIHYDROXYBENZOIC ACID	3
2AF	2-AMINOPHENOL	2
4NC	4-NITROCATECHOL	2
2X7	(3E)-3-iminooxepin-2(3H)-one	1
2XP	(2Z,4Z)-2-imino-6-oxohex-4-enoic acid	1
CL	CHLORIDE ION	1
OH	HYDROXIDE ION	1