X-group (possible homology)

140 Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases

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Ligands and drugs

4,544

Member domains

201

with ligand contacts (≤ 4 Å)

4.4% of members

154

with DrugDomain annotations

3.4% of members

with a DrugBank compound

2.1% 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)

6.8

Superclasses per 20 proteins

narrower than 63% 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	14	6.5	2.14×	q = 4.2e-3
Homogeneous non-metal compounds	2	5.1	0.39×	q = 0.20
Homogeneous metal compounds	3	11.6	0.26×	q = 8.8e-4
Lipids and lipid-like molecules	3	2.6	1.14×	not tested
Organic acids and derivatives	4	3.7	1.09×	not tested
Organic oxygen compounds	2	4.7	0.42×	not tested
Organoheterocyclic compounds	1	3.6	0.28×	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
DB00134	MET	Methionine	28
DB00410	MRC	Mupirocin	6
DB00171	ATP	ATP	5
DB02916	LMS	[(2r,3s,4r,5r)-5-(6-Amino-9h-Purin-9-Yl)-3,4-Dihydroxytetrahydro-2-Furanyl]Methyl Sulfamate	5
DB02831	2HP	Dihydrogenphosphate	4
DB02229	MSP	5'-O-[(L-methionyl)-sulphamoyl]adenosine	3
DB00151	—	Cysteine	2
DB00167	—	Isoleucine	2
DB02684	5CA	5'-O-(L-Cysteinylsulfamoyl)adenosine	2
DB00125	ARG	Arginine	1
DB00131	AMP	Adenosine phosphate	1
DB00149	—	Leucine	1
DB00161	—	Valine	1
DB01755	ILA	N-[Isoleucinyl]-N'-[adenosyl]-diaminosufone	1

Most frequently bound compounds

PDB ligand	Name	Domains in contact
LSS	5'-O-(L-leucylsulfamoyl)adenosine	19
ATP	ADENOSINE-5'-TRIPHOSPHATE	11
ILA	N-[ISOLEUCINYL]-N'-[ADENOSYL]-DIAMINOSUFONE	8
LMS	[(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDRO-2-FURANYL]METHYL SULFAMATE	8
MRC	MUPIROCIN	8
GSU	O5'-(L-GLUTAMYL-SULFAMOYL)-ADENOSINE	6
MGmetal	MAGNESIUM ION	6
AMP	ADENOSINE MONOPHOSPHATE	5
2HP	DIHYDROGENPHOSPHATE ION	4
USB	[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] (2~{S})-2-azanyl-4-methyl-pentanoate	4
VAA	N-[VALINYL]-N'-[ADENOSYL]-DIAMINOSUFONE	4
CL	CHLORIDE ION	3
MSP	5'-O-[(L-METHIONYL)-SULPHAMOYL]ADENOSINE	3
TAR	D(-)-TARTARIC ACID	3
5CA	5'-O-(N-(L-CYSTEINYL)-SULFAMOYL)ADENOSINE	2
5GP	GUANOSINE-5'-MONOPHOSPHATE	2
84T	[(2S,4S,5R)-5-(6-aminopurin-9-yl)-4-oxidanyl-oxolan-2-yl]methoxy-N-[(2S,3R)-4-methyl-2,3-bis(oxidanyl)pentanoyl]phosphonamidic acid	2
A1CYZ	5'-O-[(R)-{[(2R)-2-amino-3-sulfanylpropanoyl]oxy}(hydroxy)phosphoryl]adenosine	2
ADP	ADENOSINE-5'-DIPHOSPHATE	2
GV6	[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] (2S,3S)-2-azanyl-3-methyl-pentanoate	2