X-group (possible homology)

2011 Phosphorylase/hydrolase-like

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Ligands and drugs

8,880

Member domains

3,284

with ligand contacts (≤ 4 Å)

37.0% of members

3,010

with DrugDomain annotations

33.9% of members

2,387

with a DrugBank compound

26.9% 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.

294

Proteins with classified ligands

Superclasses bound (of 23)

8.3

Superclasses per 20 proteins

broader than 62% 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
Organoheterocyclic compounds	88	44.6	1.97×	q < 0.0001
Homogeneous metal compounds	199	142.3	1.40×	q < 0.0001
Organic acids and derivatives	59	44.9	1.31×	q = 0.05
Homogeneous non-metal compounds	64	62.4	1.03×	q = 0.88
Phenylpropanoids and polyketides	6	6.0	0.99×	q = 1.00
Benzenoids	18	21.2	0.85×	q = 0.65
Organosulfur compounds	5	6.0	0.84×	q = 1.00
Organic oxygen compounds	44	57.7	0.76×	q = 0.07
Mixed metal/non-metal compounds	4	6.1	0.66×	q = 0.62
Nucleosides, nucleotides, and analogues	34	80.1	0.42×	q < 0.0001
Organic nitrogen compounds	3	9.3	0.32×	q = 0.05
Lipids and lipid-like molecules	8	32.3	0.25×	q < 0.0001
Miscellaneous inorganic compounds	1	0.2	4.62×	not tested
Organic 1,3-dipolar compounds	1	0.2	4.12×	not tested
Alkaloids and derivatives	1	1.0	1.01×	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	144
DB00173	ADE	Adenine	87
DB03419	URA	Uracil	77
DB03424	BES	Ubenimex	47
DB03101	R1P	Ribose-1-Phosphate	46
DB02281	FMC	Formycin	44
DB04485	THM	Thymidine	44
DB04076	HPA	Hypoxanthine	41
DB02256	DUR	2'-Deoxyuridine	36
DB02282	MTA	5'-S-methyl-5'-thioadenosine	35
DB03551	DIH	(3R,4R)-3-Hydroxy-4-(hydroxymethyl)-1-[(4-oxo-4,4a,5,7a-tetrahydro-3H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]pyrrolidinium	35
DB00640	ADN	Adenosine	34
DB00544	URF	Fluorouracil	32
DB02681	V7O	2,8-bis[oxido(oxo)vanadio]-1,1,1,3,5,5,7,7,9,9,9-undecaoxopentavanadoxane-2,8-diium	30
DB02745	URI	Uridine	27
DB06185	IMH	Forodesine	26
DB03462	TDR	Thymine	22
DB04627	ANU	Cyclouridine	22
DB02377	GUN	Guanine	18
DB07437	BAU	5-Benzylacyclouridine	17

Most frequently bound compounds

PDB ligand	Name	Domains in contact
ZNmetal	ZINC ION	1,331
CL	CHLORIDE ION	311
CAmetal	CALCIUM ION	209
NAmetal	SODIUM ION	200
Kmetal	POTASSIUM ION	164
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	154
MNmetal	MANGANESE (II) ION	133
ADE	ADENINE	94
MGmetal	MAGNESIUM ION	89
URA	URACIL	76
COmetal	COBALT (II) ION	51
BES	2-(3-AMINO-2-HYDROXY-4-PHENYL-BUTYRYLAMINO)-4-METHYL-PENTANOIC ACID	47
MTA	5'-DEOXY-5'-METHYLTHIOADENOSINE	47
R1P	1-O-phosphono-alpha-D-ribofuranose	45
FMC	(1S)-1-(7-amino-1H-pyrazolo[4,3-d]pyrimidin-3-yl)-1,4-anhydro-D-ribitol	44
THM	THYMIDINE	44
IM5	2-amino-7-{[(3R,4R)-3-hydroxy-4-(hydroxymethyl)pyrrolidin-1-yl]methyl}-3,5-dihydro-4H-pyrrolo[3,2-d]pyrimidin-4-one	42
HPA	HYPOXANTHINE	40
ADN	ADENOSINE	39
DUR	2'-DEOXYURIDINE	36