X-group (possible homology)

312 HIT-like

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Ligands and drugs

1,326

Member domains

374

with ligand contacts (≤ 4 Å)

28.2% of members

387

with DrugDomain annotations

29.2% of members

269

with a DrugBank compound

20.3% 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	21	10.9	1.93×	q = 2.4e-3
Homogeneous non-metal compounds	11	8.5	1.30×	q = 0.41
Homogeneous metal compounds	24	19.4	1.24×	q = 0.21
Organic oxygen compounds	6	7.9	0.76×	q = 0.64
Organoheterocyclic compounds	4	6.1	0.66×	q = 0.59
Organic acids and derivatives	1	6.1	0.16×	q = 0.04
Organosulfur compounds	3	0.8	3.70×	not tested
Organic nitrogen compounds	1	1.3	0.80×	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
DB00131	AMP	Adenosine phosphate	60
DB01972	5GP	Guanosine-5'-Monophosphate	20
DB03345	BME	Mercaptoethanol	13
DB00118	SAM	Ademetionine	10
DB00640	ADN	Adenosine	10
DB03685	U5P	Uridine monophosphate	10
DB01861	UPG	Uridine diphosphate glucose	8
DB03501	GDU	Galactose-uridine-5'-diphosphate	8
DB01960	M7G	7-methyl-7,8-dihydroguanosine-5'-diphosphate	6
DB03435	UDP	Uridine-5'-Diphosphate	6
DB04137	GTP	Guanosine-5'-Triphosphate	5
DB01774	ADQ	Adenosine-5'-Monophosphate Glucopyranosyl-Monophosphate Ester	4
DB02843	G1P	alpha-D-glucose-1-phosphate	4
DB04457	DGP	2'-Deoxyguanosine-5'-Monophosphate	4
DB04566	IMP	Inosinic Acid	4
DB00127	SPM	Spermine	3
DB03148	AP2	Adenosine 5'-methylenediphosphate	3
DB00369	L8P	Cidofovir	2
DB01649	GTA	7-methyl-GpppA	2
DB01717	AP5	Bis(Adenosine)-5'-Pentaphosphate	2

Most frequently bound compounds

PDB ligand	Name	Domains in contact
ZNmetal	ZINC ION	79
AMP	ADENOSINE MONOPHOSPHATE	55
CL	CHLORIDE ION	40
5GP	GUANOSINE-5'-MONOPHOSPHATE	18
NAmetal	SODIUM ION	18
FEmetal	FE (III) ION	16
BME	BETA-MERCAPTOETHANOL	15
GDU	GALACTOSE-URIDINE-5'-DIPHOSPHATE	8
Kmetal	POTASSIUM ION	8
ADN	ADENOSINE	7
B4P	BIS(ADENOSINE)-5'-TETRAPHOSPHATE	7
M7G	7N-METHYL-8-HYDROGUANOSINE-5'-DIPHOSPHATE	6
SAM	S-ADENOSYLMETHIONINE	6
GTP	GUANOSINE-5'-TRIPHOSPHATE	5
UDP	URIDINE-5'-DIPHOSPHATE	5
6BI	[(2~{R},3~{S},4~{R},5~{R})-5-[6-(ethylamino)purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen phosphate	4
ADQ	ADENOSINE-5'-DIPHOSPHATE-GLUCOSE	4
G1P	1-O-phosphono-alpha-D-glucopyranose	4
U5P	URIDINE-5'-MONOPHOSPHATE	4
UNL	Unknown ligand	4