X-group (possible homology)

862 Prim-pol domain

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Ligands and drugs

365

Member domains

with ligand contacts (≤ 4 Å)

24.7% of members

with DrugDomain annotations

21.1% of members

with a DrugBank compound

13.4% 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
Homogeneous metal compounds	12	6.8	1.77×	q = 0.01
Nucleosides, nucleotides, and analogues	8	3.8	2.10×	not tested
Homogeneous non-metal compounds	3	3.0	1.01×	not tested
Organic oxygen compounds	1	2.8	0.36×	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
DB03222	DTP	dATP	14
DB04005	UTP	Uridine 5'-triphosphate	6
DB00171	ATP	ATP	4
DB02181	DGT	2'-Deoxyguanosine-5'-Triphosphate	3
DB02596	APC	alpha,beta-Methyleneadenosine 5'-triphosphate	2
DB03258	DCP	2'-Deoxycytidine 5'-triphosphate	2
DB04137	GTP	Guanosine-5'-Triphosphate	1
DB04160	PPV	Pyrophosphoric acid	1

Most frequently bound compounds

PDB ligand	Name	Domains in contact
ZNmetal	ZINC ION	49
MNmetal	MANGANESE (II) ION	28
CAmetal	CALCIUM ION	14
DTP	2'-DEOXYADENOSINE 5'-TRIPHOSPHATE	14
ATP	ADENOSINE-5'-TRIPHOSPHATE	6
UTP	URIDINE 5'-TRIPHOSPHATE	6
MGmetal	MAGNESIUM ION	4
DGT	2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE	3
2KH	5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]uridine	2
APC	DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER	2
CDmetal	CADMIUM ION	2
CL	CHLORIDE ION	2
DCP	2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE	2
HEJ	9-{5-O-[(S)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-arabinofuranosyl}-9H-purin-6-amine	2
HFD	2-fluoro-9-{5-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-arabinofuranosyl}-9H-purin-6-amine	2
JSQ	2-fluoro-ATP	2
DPO	DIPHOSPHATE	1
GTP	GUANOSINE-5'-TRIPHOSPHATE	1
NAmetal	SODIUM ION	1
PPV	PYROPHOSPHATE	1