X-group (possible homology)

7569 Uracil-DNA glycosylase-like

Open in classification tree →

Ligands and drugs

986

Member domains

215

with ligand contacts (≤ 4 Å)

21.8% of members

206

with DrugDomain annotations

20.9% of members

166

with a DrugBank compound

16.8% 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)

8.5

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
Nucleosides, nucleotides, and analogues	3	6.3	0.48×	q = 0.22
Homogeneous metal compounds	3	11.1	0.27×	q = 1.4e-3
Organic 1,3-dipolar compounds	1	0.0	53×	not tested
Organosulfur compounds	3	0.5	6.43×	not tested
Organoheterocyclic compounds	15	3.5	4.30×	not tested
Homogeneous non-metal compounds	11	4.9	2.25×	not tested
Benzenoids	1	1.7	0.60×	not tested
Lipids and lipid-like molecules	1	2.5	0.40×	not tested
Organic acids and derivatives	1	3.5	0.28×	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
DB03419	URA	Uracil	52
DB02134	XAN	Xanthine	5
DB03345	BME	Mercaptoethanol	5
DB00544	URF	Fluorouracil	4
DB02831	2HP	Dihydrogenphosphate	3
DB03800	DU	Deoxyuridine monophosphate	2
DB03904	URE	Urea	2
DB02256	DUR	2'-Deoxyuridine	1
DB02262	ORO	Orotic acid	1
DB02406	LEA	N-Valeric Acid	1
DB03792	WBU	5-Aminouracil	1
DB06990	302	4-[(1E,7E)-8-(2,6-DIOXO-1,2,3,6-TETRAHYDROPYRIMIDIN-4-YL)-3,6-DIOXA-2,7-DIAZAOCTA-1,7-DIEN-1-YL]BENZOIC ACID	1
DB07760	FCF	3-[(1E,7E)-8-(2,6-dioxo-1,2,3,6-tetrahydropyrimidin-4-yl)-3,6-dioxa-2,7-diazaocta-1,7-dien-1-yl]benzoic acid	1
DB08844	URC	Uric acid	1
DB11898	OD3	2,4-thiazolidinedione	1

Most frequently bound compounds

PDB ligand	Name	Domains in contact
URA	URACIL	52
CL	CHLORIDE ION	47
SF4	IRON/SULFUR CLUSTER	42
Kmetal	POTASSIUM ION	9
IOD	IODIDE ION	5
NAmetal	SODIUM ION	5
URF	5-FLUOROURACIL	5
XAN	XANTHINE	5
BME	BETA-MERCAPTOETHANOL	4
BR8	BARBITURIC ACID	4
SCN	THIOCYANATE ION	4
2HP	DIHYDROGENPHOSPHATE ION	3
MGmetal	MAGNESIUM ION	3
ODF	5-oxidanyl-1~{H}-pyrimidine-2,4-dione	3
3FL	3-{[(4-{[(2,6-dioxo-1,2,3,6-tetrahydropyrimidin-4-yl)methyl]amino}butyl)amino]methyl}benzoic acid	2
5CU	2,4-dioxo-1,2,3,4-tetrahydropyrimidine-5-carboxylic acid	2
5NU	5-nitrouracil	2
6UA	6-aminopyrimidine-2,4(3H,5H)-dione	2
DU	2'-DEOXYURIDINE-5'-MONOPHOSPHATE	2
HMU	5-HYDROXYMETHYL URACIL	2