X-group (possible homology)

7516 Nucleotide-diphospho-sugar transferases

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Ligands and drugs

10,208

Member domains

1,887

with ligand contacts (≤ 4 Å)

18.5% of members

1,647

with DrugDomain annotations

16.1% of members

1,383

with a DrugBank compound

13.5% 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.

163

Proteins with classified ligands

Superclasses bound (of 23)

8.0

Superclasses per 20 proteins

broader than 59% 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	132	44.4	2.97×	q < 0.0001
Organic oxygen compounds	60	32.0	1.88×	q < 0.0001
Homogeneous metal compounds	125	78.9	1.58×	q < 0.0001
Homogeneous non-metal compounds	42	34.6	1.21×	q = 0.24
Benzenoids	7	11.8	0.60×	q = 0.23
Organic nitrogen compounds	3	5.1	0.58×	q = 0.58
Organoheterocyclic compounds	11	24.7	0.45×	q = 3.3e-3
Organic acids and derivatives	9	24.9	0.36×	q = 5.2e-4
Lipids and lipid-like molecules	3	17.9	0.17×	q < 0.0001
Organometallic compounds	3	0.2	13×	not tested
Organosulfur compounds	4	3.3	1.21×	not tested
Phenylpropanoids and polyketides	3	3.3	0.90×	not tested
Hydrocarbons	1	1.1	0.89×	not tested
Mixed metal/non-metal compounds	1	3.4	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
DB03435	UDP	Uridine-5'-Diphosphate	321
DB00141	NAG	N-Acetylglucosamine	88
DB01861	UPG	Uridine diphosphate glucose	83
DB03397	UD1	Uridine-Diphosphate-N-Acetylglucosamine	68
DB04137	GTP	Guanosine-5'-Triphosphate	35
DB04315	GDP	Guanosine-5'-Diphosphate	35
DB03501	GDU	Galactose-uridine-5'-diphosphate	31
DB02196	UD2	Uridine-Diphosphate-N-Acetylgalactosamine	30
DB00131	AMP	Adenosine phosphate	28
DB02843	G1P	alpha-D-glucose-1-phosphate	28
DB02431	CTP	Cytidine-5'-Triphosphate	27
DB02696	UDH	6-Aminohexyl-uridine-C1,5'-diphosphate	25
DB03751	DAU	2'deoxy-Thymidine-5'-Diphospho-Alpha-D-Glucose	23
DB04485	THM	Thymidine	21
DB04551	FBP	beta-D-fructofuranose 1,6-bisphosphate	20
DB05869	9X7	Ethyl pyruvate	20
DB02452	TTP	Thymidine 5'-triphosphate	18
DB03103	TYD	Thymidine-5'- Diphosphate	18
DB04005	UTP	Uridine 5'-triphosphate	17
DB03567	A2G	alpha-N-Acetyl-D-galactosamine	15

Most frequently bound compounds

PDB ligand	Name	Domains in contact
MNmetal	MANGANESE (II) ION	545
UDP	URIDINE-5'-DIPHOSPHATE	394
CL	CHLORIDE ION	239
MGmetal	MAGNESIUM ION	232
UPG	URIDINE-5'-DIPHOSPHATE-GLUCOSE	106
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	99
UD1	URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE	68
HGmetal	MERCURY (II) ION	48
CAmetal	CALCIUM ION	46
GDP	GUANOSINE-5'-DIPHOSPHATE	38
GTP	GUANOSINE-5'-TRIPHOSPHATE	38
FQ8	[(2~{R},3~{S},4~{S})-2,3,4,5-tetrakis(oxidanyl)pentyl] [(2~{R},3~{R},4~{S})-2,3,4-tris(oxidanyl)-5-[oxidanyl-[(2~{R},3~{S},4~{S})-2,3,4-tris(oxidanyl)-5-phosphonooxy-pentoxy]phosphoryl]oxy-pentyl] hydrogen phosphate	36
GDU	GALACTOSE-URIDINE-5'-DIPHOSPHATE	35
GDD	GUANOSINE-5'-DIPHOSPHATE-ALPHA-D-MANNOSE	34
CTP	CYTIDINE-5'-TRIPHOSPHATE	33
GAL	beta-D-galactopyranose	33
NAmetal	SODIUM ION	32
UD2	URIDINE-DIPHOSPHATE-N-ACETYLGALACTOSAMINE	29
AMP	ADENOSINE MONOPHOSPHATE	28
G1P	1-O-phosphono-alpha-D-glucopyranose	28