X-group (possible homology)

239 Ribosomal protein L25-like

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Ligands and drugs

7,053

Member domains

999

with ligand contacts (≤ 4 Å)

14.2% of members

759

with DrugDomain annotations

10.8% of members

338

with a DrugBank compound

4.8% 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
Organic acids and derivatives	15	7.8	1.93×	q = 0.02
Homogeneous metal compounds	36	24.7	1.46×	q = 4.1e-3
Nucleosides, nucleotides, and analogues	15	13.9	1.08×	q = 0.82
Homogeneous non-metal compounds	6	10.8	0.55×	q = 0.17
Lipids and lipid-like molecules	0	5.6	0	q = 0.01
Organic oxygen compounds	0	10.0	0	q < 0.0001
Organoheterocyclic compounds	0	7.7	0	q = 1.4e-3
Mixed metal/non-metal compounds	4	1.1	3.79×	not tested
Organic nitrogen compounds	1	1.6	0.62×	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	118
DB00130	GLN	L-Glutamine	96
DB00131	AMP	Adenosine phosphate	41
DB02663	PPQ	2-Amino-4-(Hydroxymethyl-Phosphinyl)Butanoic Acid	15
DB00142	GLU	Glutamic acid	8
DB00171	ATP	ATP	7
DB08818	—	—	5
DB00120	PHE	Phenylalanine	3
DB14103	MSL	Methionine sulfoximine	3
DB02510	—	5'-O-(L-Prolylsulfamoyl)adenosine	2
DB02684	—	5'-O-(L-Cysteinylsulfamoyl)adenosine	2
DB03566	SPD	Spermidine	2
DB03909	ACP	Adenosine-5'-[Beta, Gamma-Methylene]Triphosphate	1

Most frequently bound compounds

PDB ligand	Name	Domains in contact
MGmetal	MAGNESIUM ION	479
P3S	L-METHIONINE-S-SULFOXIMINE PHOSPHATE	94
GLN	GLUTAMINE	86
OHX	osmium (III) hexammine	84
CL	CHLORIDE ION	65
ADP	ADENOSINE-5'-DIPHOSPHATE	56
AKG	2-OXOGLUTARIC ACID	48
ATP	ADENOSINE-5'-TRIPHOSPHATE	28
PEB	PHYCOERYTHROBILIN	28
NImetal	NICKEL (II) ION	24
P3P	(2S)-2-AMINO-4-[METHYL(PHOSPHONOOXY)PHOSPHORYL]BUTANOIC ACID	20
NAmetal	SODIUM ION	12
TLmetal	THALLIUM (I) ION	12
ZNmetal	ZINC ION	12
MSL	(2S)-2-AMINO-4-(METHYLSULFONIMIDOYL)BUTANOIC ACID	10
ANP	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER	7
CAmetal	CALCIUM ION	7
AMP	ADENOSINE MONOPHOSPHATE	5
Kmetal	POTASSIUM ION	5
CDmetal	CADMIUM ION	4