X-group (possible homology)

7544 Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain

Open in classification tree →

Ligands and drugs

994

Member domains

166

with ligand contacts (≤ 4 Å)

16.7% of members

166

with DrugDomain annotations

16.7% of members

143

with a DrugBank compound

14.4% 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)

—

Superclasses per 20 proteins

fewer than 20 proteins: too few to compare at equal depth

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
Homogeneous metal compounds	8	8.2	0.97×	q = 1.00
Benzenoids	6	1.2	4.90×	not tested
Organic nitrogen compounds	1	0.5	1.87×	not tested
Organic oxygen compounds	6	3.3	1.80×	not tested
Homogeneous non-metal compounds	6	3.6	1.66×	not tested
Organoheterocyclic compounds	3	2.6	1.16×	not tested
Nucleosides, nucleotides, and analogues	5	4.6	1.08×	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
DB01632	PRP	5-O-phosphono-alpha-D-ribofuranosyl diphosphate	69
DB04166	BE2	Anthranilic acid	15
DB00936	SAL	Salicylic acid	4
DB03462	TDR	Thymine	4
DB04485	THM	Thymidine	3
DB00131	AMP	Adenosine phosphate	2
DB02097	CTN	Cytidine	2
DB02745	URI	Uridine	2
DB03554	IUR	5-Iodouracil	2
DB00495	AZZ	Zidovudine	1
DB02219	CXS	3-(cyclohexylamino)propanesulfonic acid	1
DB03419	URA	Uracil	1
DB09343	—	—	1

Most frequently bound compounds

PDB ligand	Name	Domains in contact
MGmetal	MAGNESIUM ION	73
PRP	1-O-pyrophosphono-5-O-phosphono-alpha-D-ribofuranose	69
BE2	2-AMINOBENZOIC ACID	15
POP	PYROPHOSPHATE 2-	10
17C	2,2'-iminodibenzoic acid	6
FA0	2-amino-4-fluorobenzoic acid	6
MNmetal	MANGANESE (II) ION	6
14B	2-amino-3,5-dimethylbenzoic acid	4
17D	2-benzylbenzoic acid	4
CL	CHLORIDE ION	4
SAL	2-HYDROXYBENZOIC ACID	4
TA7	4,4,4-trifluoro-1-(4-methoxyphenyl)butane-1,3-dione	4
7P3	2-[(2-carboxyphenyl)amino]-5-[(5-phosphonopentyl)oxy]benzoic acid	3
NAmetal	SODIUM ION	3
TDR	THYMINE	3
THM	THYMIDINE	3
17N	8-methoxyphenanthro[3,4-d][1,3]dioxole-5,6-dicarboxylic acid	2
3F0	2-azanyl-3-fluoranyl-benzoic acid	2
3M0	2-azanyl-3-methyl-benzoic acid	2
4M0	2-azanyl-4-methyl-benzoic acid	2