X-group (possible homology)

245 Ribonuclease PH domain 2-like

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Ligands and drugs

3,435

Member domains

147

with ligand contacts (≤ 4 Å)

4.3% of members

129

with DrugDomain annotations

3.8% of members

with a DrugBank compound

2.7% 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	5	5.8	0.86×	q = 0.84
Mixed metal/non-metal compounds	2	0.3	8.05×	not tested
Organic nitrogen compounds	1	0.4	2.65×	not tested
Homogeneous non-metal compounds	3	2.6	1.18×	not tested
Nucleosides, nucleotides, and analogues	2	3.3	0.61×	not tested
Organic oxygen compounds	1	2.4	0.42×	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
DB16833	ADP	Adenosine disphosphate	13
DB00131	AMP	Adenosine phosphate	7
DB04160	PPV	Pyrophosphoric acid	6
DB03685	U5P	Uridine monophosphate	5
DB04237	TAM	Tris(Hydroxyethyl)Aminomethane	2
DB03435	UDP	Uridine-5'-Diphosphate	1
DB04352	RP5	beta-D-Ribose-5-phosphate	1
DB04555	CDP	Cytidine-5'-Diphosphate	1

Most frequently bound compounds

PDB ligand	Name	Domains in contact
MGmetal	MAGNESIUM ION	16
ADP	ADENOSINE-5'-DIPHOSPHATE	13
WO4	TUNGSTATE(VI)ION	13
AMP	ADENOSINE MONOPHOSPHATE	7
PPV	PYROPHOSPHATE	6
U5P	URIDINE-5'-MONOPHOSPHATE	5
CDmetal	CADMIUM ION	3
BR	BROMIDE ION	2
NAmetal	SODIUM ION	2
TAM	TRIS(HYDROXYETHYL)AMINOMETHANE	2
UNX	UNKNOWN ATOM OR ION	2
CDP	CYTIDINE-5'-DIPHOSPHATE	1
MNmetal	MANGANESE (II) ION	1
RP5	5-O-phosphono-beta-D-ribofuranose	1
UDP	URIDINE-5'-DIPHOSPHATE	1