X-group (possible homology)

7573 PRTase-like

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Ligands and drugs

4,750

Member domains

1,174

with ligand contacts (≤ 4 Å)

24.7% of members

1,066

with DrugDomain annotations

22.4% of members

855

with a DrugBank compound

18.0% 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)

6.3

Superclasses per 20 proteins

narrower 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
Organoheterocyclic compounds	31	14.1	2.20×	q < 0.0001
Nucleosides, nucleotides, and analogues	53	25.4	2.09×	q < 0.0001
Organic oxygen compounds	25	18.3	1.37×	q = 0.13
Homogeneous non-metal compounds	27	19.7	1.37×	q = 0.11
Homogeneous metal compounds	53	45.0	1.18×	q = 0.17
Organic acids and derivatives	3	14.2	0.21×	q = 1.1e-3
Benzenoids	0	6.7	0	q = 4.3e-3
Lipids and lipid-like molecules	0	10.2	0	q = 1.2e-4
Organosulfur compounds	2	1.9	1.06×	not tested
Mixed metal/non-metal compounds	1	1.9	0.52×	not tested
Organic nitrogen compounds	1	2.9	0.34×	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
DB16833	ADP	Adenosine disphosphate	113
DB00171	ATP	ATP	96
DB01632	PRP	5-O-phosphono-alpha-D-ribofuranosyl diphosphate	95
DB00131	AMP	Adenosine phosphate	64
DB01972	5GP	Guanosine-5'-Monophosphate	57
DB03685	U5P	Uridine monophosphate	30
DB04566	IMP	Inosinic Acid	28
DB00173	ADE	Adenine	25
DB04022	G4P	Guanosine tetraphosphate	17
DB00437	7HP	7-HYDROXY-PYRAZOLO[4,3-D]PYRIMIDINE	12
DB03942	PCP	Carboxylic PRPP	12
DB02309	XMP	5-monophosphate-9-beta-D-ribofuranosyl xanthine	11
DB04137	GTP	Guanosine-5'-Triphosphate	10
DB02262	ORO	Orotic acid	9
DB03419	URA	Uracil	9
DB02053	R5P	Ribose-5-phosphate	8
DB02431	CTP	Cytidine-5'-Triphosphate	8
DB02798	ABM	Alpha-Methylene Adenosine Monophosphate	8
DB04076	HPA	Hypoxanthine	8
DB11326	BO3	Boric acid	8

Most frequently bound compounds

PDB ligand	Name	Domains in contact
MGmetal	MAGNESIUM ION	509
HSX	5-O-phosphono-alpha-D-ribofuranose	141
ADP	ADENOSINE-5'-DIPHOSPHATE	120
ATP	ADENOSINE-5'-TRIPHOSPHATE	96
PRP	1-O-pyrophosphono-5-O-phosphono-alpha-D-ribofuranose	93
AMP	ADENOSINE MONOPHOSPHATE	64
5GP	GUANOSINE-5'-MONOPHOSPHATE	61
CL	CHLORIDE ION	60
POP	PYROPHOSPHATE 2-	40
U5P	URIDINE-5'-MONOPHOSPHATE	34
NAmetal	SODIUM ION	32
IMP	INOSINIC ACID	28
ADE	ADENINE	25
APC	DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER	23
YPG	[3-[(3~{R},4~{R})-3-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-4-[(2~{S})-2-oxidanyl-2-phosphono-ethoxy]pyrrolidin-1-yl]-3-oxidanylidene-propyl]phosphonic acid	20
G4P	GUANOSINE-5',3'-TETRAPHOSPHATE	19
3L4	[(2-{[2-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)ethyl][(E)-2-phosphonoethenyl]amino}ethoxy)methyl]phosphonic acid	14
CDmetal	CADMIUM ION	14
45T	{[(2S)-3-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)propane-1,2-diyl]bis(oxyethane-2,1-diyl)}bis(phosphonic acid)	12
7HP	7-HYDROXY-PYRAZOLO[4,3-D]PYRIMIDINE	12