X-group (possible homology)

7559 Ribosomal protein L4

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Ligands and drugs

3,403

Member domains

1,386

with ligand contacts (≤ 4 Å)

40.7% of members

620

with DrugDomain annotations

18.2% of members

with a DrugBank compound

1.1% 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)

5.2

Superclasses per 20 proteins

narrower than 80% 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	29	14.0	2.07×	q < 0.0001
Organic oxygen compounds	4	5.7	0.70×	q = 0.71
Homogeneous non-metal compounds	0	6.2	0	q = 4.7e-3
Nucleosides, nucleotides, and analogues	0	7.9	0	q = 5.5e-4
Mixed metal/non-metal compounds	2	0.6	3.33×	not tested
Organic nitrogen compounds	2	0.9	2.19×	not tested
Lipids and lipid-like molecules	1	3.2	0.31×	not tested
Organic acids and derivatives	1	4.4	0.23×	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
DB00125	ARG	Arginine	16
DB03566	SPD	Spermidine	3
DB00954	DI0	Dirithromycin	2
DB00207	ZIT	Azithromycin	1
DB00479	AKN	Amikacin	1
DB04626	AM2	Apramycin	1
DB06145	SPR	Spiramycin	1
DB11638	—	—	1

Most frequently bound compounds

PDB ligand	Name	Domains in contact
MGmetal	MAGNESIUM ION	1,365
OHX	osmium (III) hexammine	76
Kmetal	POTASSIUM ION	68
NAmetal	SODIUM ION	66
SPD	SPERMIDINE	52
ARG	ARGININE	21
ATP	ADENOSINE-5'-TRIPHOSPHATE	9
MNmetal	MANGANESE (II) ION	6
PAR	PAROMOMYCIN	6
UNX	UNKNOWN ATOM OR ION	6
PUT	1,4-DIAMINOBUTANE	5
CL	CHLORIDE ION	3
SPM	SPERMINE	3
SRmetal	STRONTIUM ION	3
LUJ	(1R,2R,3S,4R,6S)-4,6-diamino-2-{[3-O-(2,6-diamino-2,6-dideoxy-beta-L-idopyranosyl)-beta-D-ribofuranosyl]oxy}-3-hydroxycyclohexyl 2-amino-2,4-dideoxy-4-propyl-alpha-D-glucopyranoside	2
SJE	(2R,3S,4R,5R,7S,9S,10S,11R,12S,13R)-12-(((2R,4R,5S,6S)-4,5-dihydroxy-4,6-dimethyltetrahydro-2H-pyran-2-yl)oxy)-2-((S)-1-(((2R,3R,4R,5R,6R)-5-hydroxy-3,4-dimethoxy-6-methyltetrahydro-2H-pyran-2-yl)oxy)propan-2-yl)-10-(((2S,3R,4R,6R)-3-hydroxy-4-(methoxyamino)-6-methyltetrahydro-2H-pyran-2-yl)oxy)-3,5,7,9,11,13-hexamethyl-7-(((2-((2-nitrophenyl)sulfonamido)ethyl)carbamoyl)oxy)-6,14-dioxooxacyclotetradecan-4-yl 3-methylbutanoate	2
SJH	(2R,3S,4R,5R,7S,9S,10S,11R,12S,13R)-12-(((2R,4R,5S,6S)-4,5-dihydroxy-4,6-dimethyltetrahydro-2H-pyran-2-yl)oxy)-2-((S)-1-(((2R,3R,4R,5R,6R)-5-hydroxy-3,4-dimethoxy-6-methyltetrahydro-2H-pyran-2-yl)oxy)propan-2-yl)-10-(((2S,3R,6R,E)-3-hydroxy-4-(methoxyimino)-6-methyltetrahydro-2H-pyran-2-yl)oxy)-3,5,7,9,11,13-hexamethyl-7-(((2-(2-methyl-5-nitro-1H-imidazol-1-yl)ethyl)carbamoyl)oxy)-6,14-dioxooxacyclotetradecan-4-yl 3-methylbutanoate	2
WDP	Sequanamycin 9	2
84G	Arbekacin	1
AKN	(2S)-N-[(1R,2S,3S,4R,5S)-4-[(2R,3R,4S,5S,6R)-6-(aminomethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-5-azanyl-2-[(2S,3R,4S,5S,6R)-4-azanyl-6-(hydroxymethyl)-3,5-bis(oxidanyl)oxan-2-yl]oxy-3-oxidanyl-cyclohexyl]-4-azanyl-2-oxidanyl-butanamide	1