X-group (possible homology)

4969 "thumb" domain in bacteriophage RB69-like DNA polymerase I

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Ligands and drugs

668

Member domains

with ligand contacts (≤ 4 Å)

5.5% of members

with DrugDomain annotations

3.7% of members

with a DrugBank compound

1.5% 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	0.25×observed / expected4×	Ratio	Significance
Homogeneous metal compounds	5	2.9		1.72×	not tested
Organic acids and derivatives	1	0.9		1.09×	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
DB00242	—	Cladribine	4
DB00631	—	Clofarabine	2
DB01073	—	—	2
DB01280	—	—	2
DB01956	TAU	Taurine	1

Most frequently bound compounds

PDB ligand	Name	Domains in contact
CAmetal	CALCIUM ION	17
Kmetal	POTASSIUM ION	3
MGmetal	MAGNESIUM ION	2
MNmetal	MANGANESE (II) ION	2
BR	BROMIDE ION	1
NAmetal	SODIUM ION	1
TAU	2-AMINOETHANESULFONIC ACID	1