X-group (possible homology)

4954 central helical domain in RNA-polymerase beta-prime subunit

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Ligands and drugs

2,167

Member domains

582

with ligand contacts (≤ 4 Å)

26.9% of members

401

with DrugDomain annotations

18.5% of members

with a DrugBank compound

2.0% 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)

6.7

Superclasses per 20 proteins

narrower than 66% 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	27	14.5	1.86×	q < 0.0001
Organic oxygen compounds	5	5.9	0.85×	q = 0.88
Nucleosides, nucleotides, and analogues	5	8.2	0.61×	q = 0.29
Homogeneous non-metal compounds	0	6.4	0	q = 2.9e-3
Benzenoids	3	2.2	1.39×	not tested
Lipids and lipid-like molecules	2	3.3	0.61×	not tested
Organoheterocyclic compounds	2	4.6	0.44×	not tested
Organic acids and derivatives	2	4.6	0.44×	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
DB02596	APC	alpha,beta-Methyleneadenosine 5'-triphosphate	8
DB02431	CTP	Cytidine-5'-Triphosphate	5
DB04785	STD	Streptolydigin	5
DB00171	ATP	ATP	4
DB03532	G2P	Phosphomethylphosphonic acid guanylate ester	4
DB04005	UTP	Uridine 5'-triphosphate	4
DB04137	GTP	Guanosine-5'-Triphosphate	4
DB00142	GLU	Glutamic acid	2
DB04022	G4P	Guanosine tetraphosphate	2
DB08226	MXP	Myxopyronin B	2
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	2

Most frequently bound compounds

PDB ligand	Name	Domains in contact
ZNmetal	ZINC ION	540
MGmetal	MAGNESIUM ION	18
1N7	CHAPSO	9
APC	DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER	6
G2P	PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER	6
2TM	5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]cytidine	5
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
5N0	3-({3-[(3-{[4-({4-[(4-{[4-({(2R)-2-amino-4-[(1-methyl-4-{[1-methyl-4-({1-methyl-4-[(1-methyl-1H-imidazole-2-carbonyl)amino]-1H-imidazole-2-carbonyl}amino)-1H-pyrrole-2-carbonyl]amino}-1H-pyrrole-2-carbonyl)amino]butanoyl}amino)-1-methyl-1H-imidazole-2-carbonyl]amino}-1-methyl-1H-pyrrole-2-carbonyl)amino]-1-methyl-1H-pyrrole-2-carbonyl}amino)-1-methyl-1H-pyrrole-2-carbonyl]amino}propyl)(methyl)amino]propyl}carbamoyl)benzoic acid	4
ATP	ADENOSINE-5'-TRIPHOSPHATE	4
CTP	CYTIDINE-5'-TRIPHOSPHATE	4
STD	STREPTOLYDIGIN	4
UTP	URIDINE 5'-TRIPHOSPHATE	4
G4P	GUANOSINE-5',3'-TETRAPHOSPHATE	3
NE6	methyl [(1E,5R)-5-{(3S)-3-[(2E,4E)-2,5-dimethylocta-2,4-dienoyl]-2,4-dioxo-3,4-dihydro-2H-pyran-6-yl}hexylidene]carbamate	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
GLU	GLUTAMIC ACID	2
GTP	GUANOSINE-5'-TRIPHOSPHATE	2
MXP	Myxopyronin B	2
PBmetal	LEAD (II) ION	2