X-group (possible homology)

234 Microbial ribonucleases-like

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Ligands and drugs

449

Member domains

226

with ligand contacts (≤ 4 Å)

50.3% of members

227

with DrugDomain annotations

50.6% of members

178

with a DrugBank compound

39.6% 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	8	6.8	1.18×	q = 0.68
Organohalogen compounds	1	0.0	25×	not tested
Organosulfur compounds	1	0.3	3.52×	not tested
Mixed metal/non-metal compounds	1	0.3	3.45×	not tested
Nucleosides, nucleotides, and analogues	9	3.8	2.36×	not tested
Organic oxygen compounds	6	2.8	2.18×	not tested
Homogeneous non-metal compounds	3	3.0	1.01×	not tested
Organic acids and derivatives	1	2.1	0.47×	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
DB01937	2GP	Guanosine-2'-monophosphate	68
DB03315	3GP	Guanosine 3'-monophosphate	26
DB03178	SGP	Guanosine-2',3'-cyclophosphorothioate	9
DB02379	BGC	Beta-D-Glucose	5
DB02857	GMP	Guanosine	3
DB03266	PTD	Glutaral	3
DB03904	URE	Urea	3
DB03448	UM3	2'-Deoxyuridine 3'-Monophosphate	2

Most frequently bound compounds

PDB ligand	Name	Domains in contact
2GP	GUANOSINE-2'-MONOPHOSPHATE	67
CAmetal	CALCIUM ION	66
3GP	GUANOSINE-3'-MONOPHOSPHATE	24
ZNmetal	ZINC ION	23
SGP	GUANOSINE-2',3'-CYCLOPHOSPHOROTHIOATE	8
BGC	beta-D-glucopyranose	5
NAmetal	SODIUM ION	5
2AM	ADENOSINE-2'-MONOPHOSPHATE	4
CL	CHLORIDE ION	3
Kmetal	POTASSIUM ION	3
PTD	PENTANEDIAL	3
URE	UREA	3
3AM	[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-hydroxy-2-(hydroxymethyl)oxolan-3-yl] dihydrogen phosphate	2
3PD	2-AMINO-9-(2-DEOXY-3-O-PHOSPHONOPENTOFURANOSYL)-1,9-DIHYDRO-6H-PURIN-6-ONE	2
BRJ	2-BROMOETHANOL	2
CDmetal	CADMIUM ION	2
GMP	GUANOSINE	2
PGP	GUANOSINE-3',5'-DIPHOSPHATE	2
UNX	UNKNOWN ATOM OR ION	2
GPC	2'-FLUOROGUANYLYL-(3'-5')-PHOSPHOCYTIDINE	1