X-group (possible homology)

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Ligands and drugs

68,086

Member domains

18,200

with ligand contacts (≤ 4 Å)

26.7% of members

17,637

with DrugDomain annotations

25.9% of members

10,532

with a DrugBank compound

15.5% 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.

1,610

Proteins with classified ligands

Superclasses bound (of 23)

8.5

Superclasses per 20 proteins

broader than 66% 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 oxygen compounds	622	316.1	1.97×	q < 0.0001
Organic nitrogen compounds	82	50.6	1.62×	q < 0.0001
Homogeneous metal compounds	923	779.2	1.19×	q < 0.0001
Mixed metal/non-metal compounds	33	33.3	0.99×	q = 1.00
Organic acids and derivatives	234	245.6	0.95×	q = 0.52
Homogeneous non-metal compounds	299	341.7	0.88×	q = 0.01
Alkaloids and derivatives	4	5.4	0.74×	q = 0.88
Organosulfur compounds	24	32.7	0.73×	q = 0.18
Benzenoids	71	116.1	0.61×	q < 0.0001
Organoheterocyclic compounds	135	244.3	0.55×	q < 0.0001
Lipids and lipid-like molecules	94	176.8	0.53×	q < 0.0001
Phenylpropanoids and polyketides	15	33.0	0.45×	q = 1.6e-3
Hydrocarbons	3	11.1	0.27×	q = 0.02
Nucleosides, nucleotides, and analogues	116	438.8	0.26×	q < 0.0001
Lignans, neolignans and related compounds	2	1.2	1.69×	not tested
Miscellaneous inorganic compounds	1	1.2	0.84×	not tested
Organic 1,3-dipolar compounds	1	1.3	0.75×	not tested
Hydrocarbon derivatives	1	1.4	0.73×	not tested
Organohalogen compounds	2	4.5	0.44×	not tested
Organometallic compounds	1	2.3	0.44×	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
DB00141	NAG	N-Acetylglucosamine	3,264
DB08845	AKG	Oxogluric acid	511
DB00150	TRP	Tryptophan	456
DB03721	SIA	N-acetyl-alpha-neuraminic acid	276
DB02527	CMP	Cyclic adenosine monophosphate	273
DB02315	PCG	Cyclic GMP	129
DB00139	SIN	Succinic acid	113
DB02379	BGC	Beta-D-Glucose	81
DB08231	MYR	Myristic acid	80
DB03796	PLM	Palmitic Acid	77
DB01979	MMA	Methyl alpha-D-mannoside	54
DB03567	A2G	alpha-N-Acetyl-D-galactosamine	54
DB03103	TYD	Thymidine-5'- Diphosphate	51
DB04473	FUC	alpha-L-fucose	51
DB03345	BME	Mercaptoethanol	48
DB02831	2HP	Dihydrogenphosphate	42
DB00171	ATP	ATP	39
DB16881	88E	E-52862	36
DB00125	ARG	Arginine	33
DB01862	IPT	Isopropyl beta-D-thiogalactopyranoside	33

Most frequently bound compounds

PDB ligand	Name	Domains in contact
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	4,269
CAmetal	CALCIUM ION	3,766
MNmetal	MANGANESE (II) ION	1,355
CL	CHLORIDE ION	1,222
MGmetal	MAGNESIUM ION	1,136
ZNmetal	ZINC ION	932
NAmetal	SODIUM ION	856
NImetal	NICKEL (II) ION	783
FEmetal	FE (III) ION	533
AUmetal	GOLD ION	528
AKG	2-OXOGLUTARIC ACID	501
OGA	N-OXALYLGLYCINE	487
TRP	TRYPTOPHAN	456
FE2metal	FE (II) ION	406
GAL	beta-D-galactopyranose	314
CMP	ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE	288
SIA	N-acetyl-alpha-neuraminic acid	187
Kmetal	POTASSIUM ION	175
CUmetal	COPPER (II) ION	146
COmetal	COBALT (II) ION	134