X-group (possible homology)

4042 barrel domain in beta subunit of DNA dependent RNA-polymerase

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Ligands and drugs

2,332

Member domains

204

with ligand contacts (≤ 4 Å)

8.7% of members

152

with DrugDomain annotations

6.5% of members

with a DrugBank compound

3.7% 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)

—

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	6	7.7	0.78×	q = 0.54
Phenylpropanoids and polyketides	6	0.3	18×	not tested
Lipids and lipid-like molecules	4	1.8	2.28×	not tested
Organic oxygen compounds	6	3.1	1.91×	not tested
Benzenoids	2	1.2	1.73×	not tested
Nucleosides, nucleotides, and analogues	6	4.4	1.38×	not tested
Organoheterocyclic compounds	3	2.4	1.24×	not tested
Homogeneous non-metal compounds	3	3.4	0.88×	not tested
Organic acids and derivatives	2	2.4	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
DB01045	RFP	Rifampin	13
DB02596	APC	alpha,beta-Methyleneadenosine 5'-triphosphate	12
DB02431	CTP	Cytidine-5'-Triphosphate	11
DB03532	G2P	Phosphomethylphosphonic acid guanylate ester	10
DB00171	ATP	ATP	9
DB04137	GTP	Guanosine-5'-Triphosphate	7
DB04005	UTP	Uridine 5'-triphosphate	6
DB00615	RBT	Rifabutin	2
DB01201	RPT	Rifapentine	2
DB02333	DUT	Deoxyuridine-5'-Triphosphate	2
DB03170	COD	Dephospho Coenzyme A	2
DB04788	TGT	Tagetitoxin	2
DB00131	AMP	Adenosine phosphate	1
DB02181	DGT	2'-Deoxyguanosine-5'-Triphosphate	1
DB03258	DCP	2'-Deoxycytidine 5'-triphosphate	1
DB04022	G4P	Guanosine tetraphosphate	1
DB04160	PPV	Pyrophosphoric acid	1
DB14128	NAD	Nadide	1

Most frequently bound compounds

PDB ligand	Name	Domains in contact
1N7	CHAPSO	22
W0F	[[(2~{S},3~{R},4~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3-methoxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate	16
ATP	ADENOSINE-5'-TRIPHOSPHATE	14
APC	DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER	13
RFP	RIFAMPICIN	12
2TM	5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]cytidine	11
CTP	CYTIDINE-5'-TRIPHOSPHATE	10
MGmetal	MAGNESIUM ION	10
G2P	PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER	8
3AT	3'-DEOXYADENOSINE-5'-TRIPHOSPHATE	7
GTP	GUANOSINE-5'-TRIPHOSPHATE	6
UTP	URIDINE 5'-TRIPHOSPHATE	6
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	4
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	4
B4P	BIS(ADENOSINE)-5'-TETRAPHOSPHATE	4
ZNmetal	ZINC ION	4
KNG	Kanglemycin A	3
SRN	SORANGICIN A	3
1RL	Benzoxazinorifamycin-2b	2
1RM	Benzoxazinorifamycin-2c	2