X-group (possible homology)

4959 first helical domain in RNA-polymerase beta-prime subunit

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Ligands and drugs

2,219

Member domains

107

with ligand contacts (≤ 4 Å)

4.8% of members

with DrugDomain annotations

3.8% of members

with a DrugBank compound

1.4% 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
Organic acids and derivatives	2	1.2	1.64×	not tested
Homogeneous metal compounds	6	3.9	1.55×	not tested
Nucleosides, nucleotides, and analogues	3	2.2	1.38×	not tested
Organoheterocyclic compounds	1	1.2	0.82×	not tested
Organic oxygen compounds	1	1.6	0.64×	not tested
Homogeneous non-metal compounds	1	1.7	0.59×	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
DB04022	G4P	Guanosine tetraphosphate	10
DB02431	CTP	Cytidine-5'-Triphosphate	4
DB02596	APC	alpha,beta-Methyleneadenosine 5'-triphosphate	4
DB00156	THR	Threonine	2
DB00171	ATP	ATP	2
DB04005	UTP	Uridine 5'-triphosphate	2
DB04137	GTP	Guanosine-5'-Triphosphate	2
DB04788	TGT	Tagetitoxin	2
DB03258	DCP	2'-Deoxycytidine 5'-triphosphate	1

Most frequently bound compounds

PDB ligand	Name	Domains in contact
MGmetal	MAGNESIUM ION	62
1N7	CHAPSO	14
G4P	GUANOSINE-5',3'-TETRAPHOSPHATE	12
2TM	5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]cytidine	6
APC	DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER	5
ZNmetal	ZINC ION	3
TGT	TAGETITOXIN	2
0O2	guanosine 5'-(tetrahydrogen triphosphate) 3'-(trihydrogen diphosphate)	1
A1L89	P1-(5'-Adenosyl) P4-(5'-uridyl) tetraphosphate	1
ATP	ADENOSINE-5'-TRIPHOSPHATE	1
CTP	CYTIDINE-5'-TRIPHOSPHATE	1
G2P	PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER	1
POP	PYROPHOSPHATE 2-	1
UTP	URIDINE 5'-TRIPHOSPHATE	1