X-group (possible homology)

2490 Ribosomal protein L13/L15p/L18e/L32e

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Ligands and drugs

8,566

Member domains

3,151

with ligand contacts (≤ 4 Å)

36.8% of members

1,543

with DrugDomain annotations

18.0% of members

with a DrugBank compound

0.9% 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)

4.9

Superclasses per 20 proteins

narrower than 84% 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	73	39.7	1.84×	q < 0.0001
Organic acids and derivatives	3	12.5	0.24×	q = 4.0e-3
Homogeneous non-metal compounds	4	17.4	0.23×	q = 2.0e-4
Organic oxygen compounds	2	16.1	0.12×	q < 0.0001
Organoheterocyclic compounds	1	12.4	0.08×	q = 1.2e-4
Nucleosides, nucleotides, and analogues	1	22.4	0.04×	q < 0.0001
Benzenoids	0	5.9	0	q = 8.8e-3
Lipids and lipid-like molecules	0	9.0	0	q = 3.8e-4
Organic nitrogen compounds	15	2.6	5.82×	not tested
Mixed metal/non-metal compounds	5	1.7	2.94×	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
DB03566	SPD	Spermidine	28
DB00161	VAL	Valine	6
DB01917	PUT	Putrescine	6
DB00120	PHE	Phenylalanine	2
DB01421	PAR	Paromomycin	1
DB02494	—	(S)-3-phenyllactic acid	1
DB03685	U	Uridine monophosphate	1
DB04729	LLL	Gentamicin C1a	1
DB05636	YMZ	(+)-Mefloquine	1
DB07374	—	—	1
DB08437	—	Puromycin	1

Most frequently bound compounds

PDB ligand	Name	Domains in contact
MGmetal	MAGNESIUM ION	2,775
OHX	osmium (III) hexammine	294
CL	CHLORIDE ION	267
SPD	SPERMIDINE	176
Kmetal	POTASSIUM ION	164
NAmetal	SODIUM ION	153
SRmetal	STRONTIUM ION	86
CDmetal	CADMIUM ION	65
SPM	SPERMINE	45
PUT	1,4-DIAMINOBUTANE	43
UNX	UNKNOWN ATOM OR ION	38
PAR	PAROMOMYCIN	14
MNmetal	MANGANESE (II) ION	13
NAD	NICOTINAMIDE-ADENINE-DINUCLEOTIDE	7
8UZ	TC007	2
NMY	NEOMYCIN	2
84D	Dibekacin	1
84G	Arbekacin	1
GIR	GIRODAZOLE	1
LLL	(2R,3R,4R,5R)-2-((1S,2S,3R,4S,6R)-4,6-DIAMINO-3-((2R,3R,6S)-3-AMINO-6-(AMINOMETHYL)-TETRAHYDRO-2H-PYRAN-2-YLOXY)-2-HYDROXYCYCLOHEXYLOXY)-5-METHYL-4-(METHYLAMINO)-TETRAHYDRO-2H-PYRAN-3,5-DIOL	1