X-group (possible homology)

208 Single-stranded left-handed beta-helix

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Ligands and drugs

4,772

Member domains

1,194

with ligand contacts (≤ 4 Å)

25.0% of members

1,049

with DrugDomain annotations

22.0% of members

734

with a DrugBank compound

15.4% 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.

Proteins with classified ligands

Superclasses bound (of 23)

8.7

Superclasses per 20 proteins

broader than 71% 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
Lipids and lipid-like molecules	30	10.9	2.76×	q < 0.0001
Organic acids and derivatives	22	15.1	1.46×	q = 0.10
Nucleosides, nucleotides, and analogues	36	27.0	1.33×	q = 0.09
Homogeneous non-metal compounds	25	21.0	1.19×	q = 0.40
Benzenoids	8	7.1	1.12×	q = 0.76
Homogeneous metal compounds	38	47.9	0.79×	q = 0.09
Organoheterocyclic compounds	11	15.0	0.73×	q = 0.40
Organic oxygen compounds	12	19.4	0.62×	q = 0.11
Organometallic compounds	1	0.1	7.19×	not tested
Organosulfur compounds	2	2.0	1.00×	not tested
Phenylpropanoids and polyketides	2	2.0	0.98×	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
DB01992	COA	Coenzyme A	105
DB00151	CYS	Cysteine	45
DB00131	AMP	Adenosine phosphate	28
DB05869	9X7	Ethyl pyruvate	20
DB00119	PYR	Pyruvic acid	16
DB04551	FBP	beta-D-fructofuranose 1,6-bisphosphate	15
DB03103	TYD	Thymidine-5'- Diphosphate	13
DB03912	PNS	D-pantetheine 4'-phosphate	12
DB04348	TCH	Taurocholic acid	12
DB03462	TDR	Thymine	11
DB03397	UD1	Uridine-Diphosphate-N-Acetylglucosamine	10
DB03556	PE5	2-(2-{2-[2-(2-{2-[2-(2-Ethoxy-Ethoxy)-Ethoxy]-Ethoxy}-Ethoxy)-Ethoxy]-Ethoxy}-Ethoxy)-Ethanol, Polyethyleneglycol Peg400	10
DB00133	SER	Serine	9
DB03134	NPI	L-2-aminopimelic acid	9
DB03345	BME	Mercaptoethanol	9
DB03796	PLM	Palmitic Acid	9
DB01861	UPG	Uridine diphosphate glucose	8
DB01669	VIR	Virginiamycin M1	6
DB02767	FTT	(R)-3-hydroxytetradecanoic acid	6
DB03699	SCA	Succinyl-Coenzyme A	6

Most frequently bound compounds

PDB ligand	Name	Domains in contact
CL	CHLORIDE ION	157
ZNmetal	ZINC ION	112
MGmetal	MAGNESIUM ION	110
COA	COENZYME A	109
ACO	ACETYL COENZYME *A	76
NAmetal	SODIUM ION	59
CYS	CYSTEINE	47
VFE	2-[2-(2-chlorophenyl)sulfanylethanoyl-[[4-(1,2,4-triazol-1-yl)phenyl]methyl]amino]-N-methyl-ethanamide	34
VFN	~{N}-[(5-azanyl-1,3,4-oxadiazol-2-yl)methyl]-2-(2-chlorophenyl)sulfanyl-~{N}-[(4-cyanophenyl)methyl]ethanamide	33
VFT	2-(2-chlorophenyl)sulfanyl-~{N}-[(4-cyanophenyl)methyl]-~{N}-(1~{H}-imidazol-4-ylmethyl)ethanamide	30
VFZ	~{N}-[(5-azanyl-1,3,4-oxadiazol-2-yl)methyl]-2-(2-chlorophenyl)sulfanyl-~{N}-[(6-oxidanylidene-1~{H}-pyridin-3-yl)methyl]ethanamide	30
AMP	ADENOSINE MONOPHOSPHATE	28
CAmetal	CALCIUM ION	25
O3V	3-hydroxy-7,7-dimethyl-2-phenyl-4-(thiophen-2-yl)-2,6,7,8-tetrahydro-5H-pyrazolo[3,4-b]quinolin-5-one	24
9X7	ethyl 2-oxopropanoate	20
COmetal	COBALT (II) ION	17
PYR	PYRUVIC ACID	16
COO	CROTONYL COENZYME A	14
FBP	1,6-di-O-phosphono-beta-D-fructofuranose	14
UD1	URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE	14