X-group (possible homology)

212 Ribosomal protein S5 domain 2-like

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Ligands and drugs

18,557

Member domains

2,847

with ligand contacts (≤ 4 Å)

15.3% of members

1,850

with DrugDomain annotations

10.0% of members

699

with a DrugBank compound

3.8% 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.

157

Proteins with classified ligands

Superclasses bound (of 23)

9.4

Superclasses per 20 proteins

broader than 86% 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
Nucleosides, nucleotides, and analogues	62	42.8	1.45×	q = 2.1e-3
Homogeneous metal compounds	103	76.0	1.36×	q < 0.0001
Organic acids and derivatives	24	24.0	1.00×	q = 1.00
Benzenoids	10	11.3	0.88×	q = 0.92
Homogeneous non-metal compounds	27	33.3	0.81×	q = 0.31
Organic oxygen compounds	20	30.8	0.65×	q = 0.05
Organoheterocyclic compounds	12	23.8	0.50×	q = 0.01
Lipids and lipid-like molecules	8	17.2	0.46×	q = 0.03
Mixed metal/non-metal compounds	11	3.3	3.38×	not tested
Organic nitrogen compounds	10	4.9	2.02×	not tested
Organosulfur compounds	3	3.2	0.94×	not tested
Phenylpropanoids and polyketides	3	3.2	0.93×	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	81
DB00171	ATP	ATP	44
DB00188	BO2	Bortezomib	22
DB02930	AGS	Adenosine 5'-[gamma-thio]triphosphate	18
DB03685	U5P	Uridine monophosphate	15
DB03796	PLM	Palmitic Acid	11
DB08231	MYR	Myristic acid	11
DB00131	AMP	Adenosine phosphate	9
DB00536	GAI	Guanidine	9
DB04160	PPV	Pyrophosphoric acid	8
DB04257	PAM	Palmitoleic Acid	8
DB01972	5GP	Guanosine-5'-Monophosphate	7
DB03435	UDP	Uridine-5'-Diphosphate	7
DB03566	SPD	Spermidine	7
DB01991	TUX	TU-514	6
DB04237	TAM	Tris(Hydroxyethyl)Aminomethane	6
DB07536	C90	N-{(1S,2R)-2-hydroxy-1-[(hydroxyamino)carbonyl]propyl}-4-{[4-(morpholin-4-ylmethyl)phenyl]ethynyl}benzamide	6
DB00161	VAL	Valine	5
DB00173	ADE	Adenine	5
DB03345	BME	Mercaptoethanol	5

Most frequently bound compounds

PDB ligand	Name	Domains in contact
MGmetal	MAGNESIUM ION	1,139
MNmetal	MANGANESE (II) ION	500
ZNmetal	ZINC ION	195
ANP	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER	168
5LD	[(2R)-2-hydroxy-3-(1H-1,2,4-triazol-1-yl)propyl]phosphonic acid	128
CL	CHLORIDE ION	122
ADP	ADENOSINE-5'-DIPHOSPHATE	72
OHX	osmium (III) hexammine	62
GAL	beta-D-galactopyranose	56
ATP	ADENOSINE-5'-TRIPHOSPHATE	50
3TR	3-AMINO-1,2,4-TRIAZOLE	49
IG2	(2S,3S)-2,3-dihydroxy-3-(1H-imidazol-5-yl)propyl dihydrogen phosphate	49
Kmetal	POTASSIUM ION	44
HFK	2-(1,3-benzoxazol-2-ylamino)spiro[1,6,7,8-tetrahydroquinazoline-4,1'-cyclohexane]-5-one	38
4KZ	N-[(1R)-1-(dihydroxyboranyl)-2-phenylethyl]-Nalpha-(pyrazin-2-ylcarbonyl)-L-phenylalaninamide	36
BO2	N-[(1R)-1-(DIHYDROXYBORYL)-3-METHYLBUTYL]-N-(PYRAZIN-2-YLCARBONYL)-L-PHENYLALANINAMIDE	35
GLA	alpha-D-galactopyranose	34
NAmetal	SODIUM ION	32
DP6	(3R)-3-HYDROXY-5-{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}-3-METHYLPENTANOIC ACID	31
SPD	SPERMIDINE	29