X-group (possible homology)

314 Class II aaRS and biotin synthetases

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Ligands and drugs

10,233

Member domains

1,228

with ligand contacts (≤ 4 Å)

12.0% of members

1,089

with DrugDomain annotations

10.6% of members

756

with a DrugBank compound

7.4% 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.

159

Proteins with classified ligands

Superclasses bound (of 23)

8.7

Superclasses per 20 proteins

broader than 73% 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	58	24.3	2.39×	q < 0.0001
Nucleosides, nucleotides, and analogues	103	43.3	2.38×	q < 0.0001
Organoheterocyclic compounds	44	24.1	1.82×	q = 1.7e-4
Benzenoids	20	11.5	1.75×	q = 0.02
Homogeneous metal compounds	80	77.0	1.04×	q = 0.71
Homogeneous non-metal compounds	28	33.7	0.83×	q = 0.36
Organic nitrogen compounds	4	5.0	0.80×	q = 0.88
Lipids and lipid-like molecules	5	17.5	0.29×	q = 1.4e-3
Organic oxygen compounds	6	31.2	0.19×	q < 0.0001
Phenylpropanoids and polyketides	6	3.3	1.84×	not tested
Organosulfur compounds	5	3.2	1.55×	not tested
Hydrocarbons	1	1.1	0.91×	not tested
Mixed metal/non-metal compounds	1	3.3	0.30×	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
DB00123	LYS	Lysine	121
DB00171	ATP	ATP	92
DB00172	PRO	Proline	59
DB00117	HIS	Histidine	51
DB00131	AMP	Adenosine phosphate	46
DB04866	HFG	Halofuginone	38
DB00121	BTN	Biotin	30
DB03869	SSA	5'-O-(L-Serylsulfamoyl)adenosine	29
DB03376	A5A	5'-O-(N-(Alanyl)sulfamoyl)adenosine	25
DB00120	PHE	Phenylalanine	19
DB03355	TSB	5'-O-(L-Threonylsulfamoyl)adenosine	17
DB00166	LPA	Lipoic acid	13
DB03912	PNS	D-pantetheine 4'-phosphate	13
DB00160	ALA	Alanine	12
DB00640	ADN	Adenosine	11
DB04201	HAM	Histidyl-Adenosine Monophosphate	10
DB00128	ASP	Aspartic acid	9
DB02486	HED	2-Hydroxyethyl Disulfide	9
DB02596	APC	alpha,beta-Methyleneadenosine 5'-triphosphate	9
DB00133	SER	Serine	8

Most frequently bound compounds

PDB ligand	Name	Domains in contact
MGmetal	MAGNESIUM ION	248
ZNmetal	ZINC ION	151
LYS	LYSINE	149
ATP	ADENOSINE-5'-TRIPHOSPHATE	98
ANP	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER	89
CL	CHLORIDE ION	83
PRO	PROLINE	58
AMP	ADENOSINE MONOPHOSPHATE	55
HIS	HISTIDINE	50
HFG	7-bromo-6-chloro-3-{3-[(2R,3S)-3-hydroxypiperidin-2-yl]-2-oxopropyl}quinazolin-4(3H)-one	44
NAmetal	SODIUM ION	44
CAmetal	CALCIUM ION	36
SSA	5'-O-(N-(L-SERYL)-SULFAMOYL)ADENOSINE	36
KRS	cladosporin	32
BTN	BIOTIN	29
KAA	5'-O-[(L-LYSYLAMINO)SULFONYL]ADENOSINE	29
A5A	'5'-O-(N-(L-ALANYL)-SULFAMOYL)ADENOSINE	24
BT5	BIOTINYL-5-AMP	24
G5A	5'-O-(glycylsulfamoyl)adenosine	19
PHE	PHENYLALANINE	19