X-group (possible homology)

4958 second helical domain in RNA-polymerase beta-prime subunit

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Ligands and drugs

2,317

Member domains

232

with ligand contacts (≤ 4 Å)

10.0% of members

145

with DrugDomain annotations

6.3% of members

with a DrugBank compound

3.3% 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	7	6.8	1.03×	q = 1.00
Benzenoids	4	1.0	3.96×	not tested
Organic oxygen compounds	5	2.8	1.82×	not tested
Organoheterocyclic compounds	3	2.1	1.41×	not tested
Organic acids and derivatives	3	2.1	1.41×	not tested
Nucleosides, nucleotides, and analogues	5	3.8	1.31×	not tested
Homogeneous non-metal compounds	3	3.0	1.01×	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	11
DB02431	CTP	Cytidine-5'-Triphosphate	10
DB03532	G2P	Phosphomethylphosphonic acid guanylate ester	8
DB04137	GTP	Guanosine-5'-Triphosphate	8
DB04005	UTP	Uridine 5'-triphosphate	7
DB00171	ATP	ATP	6
DB04785	STD	Streptolydigin	6
DB04022	G4P	Guanosine tetraphosphate	5
DB04160	PPV	Pyrophosphoric acid	3
DB00142	GLU	Glutamic acid	2
DB02333	DUT	Deoxyuridine-5'-Triphosphate	2
DB04788	TGT	Tagetitoxin	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
DB02181	DGT	2'-Deoxyguanosine-5'-Triphosphate	1
DB03258	DCP	2'-Deoxycytidine 5'-triphosphate	1

Most frequently bound compounds

PDB ligand	Name	Domains in contact
ZNmetal	ZINC ION	86
MGmetal	MAGNESIUM ION	24
POP	PYROPHOSPHATE 2-	11
APC	DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER	10
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	10
GTP	GUANOSINE-5'-TRIPHOSPHATE	9
2TM	5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]cytidine	8
ATP	ADENOSINE-5'-TRIPHOSPHATE	7
DPO	DIPHOSPHATE	7
G4P	GUANOSINE-5',3'-TETRAPHOSPHATE	6
STD	STREPTOLYDIGIN	6
CTP	CYTIDINE-5'-TRIPHOSPHATE	5
PPV	PYROPHOSPHATE	4
G2P	PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER	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
UTP	URIDINE 5'-TRIPHOSPHATE	3
2KH	5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]uridine	2
42S	N'-hydroxy-N-phenyl-3-(trifluoromethyl)benzenecarboximidamide	2
42T	3-{[(2,6-dichlorophenyl)carbamoyl]amino}-N-hydroxy-N'-phenyl-5-(trifluoromethyl)benzenecarboximidamide	2
42U	4-[3-(4-fluorophenyl)-1H-pyrazol-4-yl]-N-[2-(piperazin-1-yl)ethyl]-2-(trifluoromethyl)aniline	2