X-group (possible homology)

3922 Helical domain in structural maintenance of chromosomes protein 3

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Ligands and drugs

963

Member domains

with ligand contacts (≤ 4 Å)

3.0% of members

with DrugDomain annotations

1.7% of members

with a DrugBank compound

1.2% 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)

—

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
Mixed metal/non-metal compounds	1	0.1	6.90×	not tested
Nucleosides, nucleotides, and analogues	6	1.9	3.15×	not tested
Homogeneous metal compounds	5	3.4	1.48×	not tested
Homogeneous non-metal compounds	1	1.5	0.67×	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
DB16833	ADP	Adenosine disphosphate	4
DB02930	AGS	Adenosine 5'-[gamma-thio]triphosphate	3
DB00171	ATP	ATP	2
DB11638	—	—	1
DB12695	—	—	1

Most frequently bound compounds

PDB ligand	Name	Domains in contact
MGmetal	MAGNESIUM ION	8
9JE	pentane-1,5-diol	4
AGS	PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER	4
ATP	ADENOSINE-5'-TRIPHOSPHATE	4
CL	CHLORIDE ION	4
ADP	ADENOSINE-5'-DIPHOSPHATE	3
PRO	PROLINE	3
BEF	BERYLLIUM TRIFLUORIDE ION	2
TBmetal	TERBIUM(III) ION	2
YT3metal	YTTRIUM (III) ION	2
ZNmetal	ZINC ION	2
MNmetal	MANGANESE (II) ION	1