X-group (possible homology)

4246 N-terminal domain in RNA-polymerase beta-prime subunit

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Ligands and drugs

2,284

Member domains

1,107

with ligand contacts (≤ 4 Å)

48.5% of members

460

with DrugDomain annotations

20.1% of members

with a DrugBank compound

0.7% 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)

6.5

Superclasses per 20 proteins

narrower than 68% of the 256 X-groups with enough proteins to compare (median 7.6)

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	29	16.5	1.76×	q < 0.0001
Organoheterocyclic compounds	2	5.2	0.39×	q = 0.21
Organic oxygen compounds	2	6.7	0.30×	q = 0.08
Nucleosides, nucleotides, and analogues	2	9.3	0.22×	q = 6.8e-3
Organic acids and derivatives	1	5.2	0.19×	q = 0.08
Homogeneous non-metal compounds	0	7.2	0	q = 1.3e-3
Phenylpropanoids and polyketides	1	0.7	1.43×	not tested
Lipids and lipid-like molecules	4	3.7	1.07×	not tested
Benzenoids	2	2.5	0.82×	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
DB00156	THR	Threonine	2
DB00160	ALA	Alanine	2
DB08226	MXP	Myxopyronin B	2
DB00131	AMP	Adenosine phosphate	1
DB00171	ATP	ATP	1
DB03170	COD	Dephospho Coenzyme A	1
DB04457	DG	2'-Deoxyguanosine-5'-Monophosphate	1
DB08266	NE6	Methyl [(1E,5R)-5-{3-[(2E,4E)-2,5-dimethyl-2,4-octadienoyl]-2,4-dioxo-3,4-dihydro-2H-pyran-6-yl}hexylidene]carbamate	1
DB08874	FI8	Fidaxomicin	1

Most frequently bound compounds

PDB ligand	Name	Domains in contact
ZNmetal	ZINC ION	1,100
1N7	CHAPSO	20
MGmetal	MAGNESIUM ION	7
C5P	CYTIDINE-5'-MONOPHOSPHATE	6
2TM	5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]cytidine	4
FI8	Fidaxomicin	4
4QM	(3R,5S,7R,8R,9S,10S,12S,13R,14S,17R)-10,13-dimethyl-17-[(2R)-pentan-2-yl]-2,3,4,5,6,7,8,9,11,12,14,15,16,17-tetradecahydro-1H-cyclopenta[a]phenanthrene-3,7,12-triol	3
4C2	N-[3,4-dioxo-2-(4-{[4-(trifluoromethyl)benzyl]amino}piperidin-1-yl)cyclobut-1-en-1-yl]-3,5-dimethyl-1,2-oxazole-4-sulfonamide	2
4C6	3,5-dimethyl-N-{2-[4-(4-methylbenzyl)piperidin-1-yl]-3,4-dioxocyclobut-1-en-1-yl}-1,2-oxazole-4-sulfonamide	2
A1IF9	[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [[[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl] hydrogen phosphate	2
B4P	BIS(ADENOSINE)-5'-TETRAPHOSPHATE	2
C0L	methyl[(1E,5R)-5-{(3E)-3-[(2E,4E,8R,9E,12E)-1,8-dihydroxy-2,5,9-trimethyltetradeca-2,4,9,12-tetraen-1-ylidene]-2,4-dioxo-3,4-dihydro-2H-pyran-6-yl}hex-1-en-1-yl]carbamate	2
MXP	Myxopyronin B	2
PBmetal	LEAD (II) ION	2
4C4	Myxopyronin B	1
A1L89	P1-(5'-Adenosyl) P4-(5'-uridyl) tetraphosphate	1
A1L9G	P1-(5'-Adenosyl) P4-(5'-guanosyl) tetraphosphate	1
CTP	CYTIDINE-5'-TRIPHOSPHATE	1
DGP	2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE	1
G2P	PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER	1