X-group (possible homology)

2004 P-loop domains-like

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Ligands and drugs

110,464

Member domains

18,883

with ligand contacts (≤ 4 Å)

17.1% of members

18,103

with DrugDomain annotations

16.4% of members

15,996

with a DrugBank compound

14.5% 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.

1,742

Proteins with classified ligands

Superclasses bound (of 23)

7.5

Superclasses per 20 proteins

narrower than 53% 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
Mixed metal/non-metal compounds	188	36.1	5.21×	q < 0.0001
Nucleosides, nucleotides, and analogues	1,576	474.8	3.32×	q < 0.0001
Homogeneous metal compounds	1,263	843.1	1.50×	q < 0.0001
Organosulfur compounds	26	35.3	0.74×	q = 0.17
Homogeneous non-metal compounds	224	369.7	0.61×	q < 0.0001
Alkaloids and derivatives	3	5.9	0.51×	q = 0.37
Benzenoids	56	125.6	0.45×	q < 0.0001
Organic nitrogen compounds	22	54.8	0.40×	q < 0.0001
Phenylpropanoids and polyketides	14	35.7	0.39×	q = 1.4e-4
Organic oxygen compounds	109	342.0	0.32×	q < 0.0001
Organic acids and derivatives	83	265.8	0.31×	q < 0.0001
Lipids and lipid-like molecules	55	191.2	0.29×	q < 0.0001
Organoheterocyclic compounds	72	264.3	0.27×	q < 0.0001
Hydrocarbons	2	12.0	0.17×	q = 2.3e-3
Organohalogen compounds	3	4.9	0.61×	not tested
Organometallic compounds	1	2.5	0.41×	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	4,725
DB00171	ATP	ATP	3,189
DB04315	GDP	Guanosine-5'-Diphosphate	1,827
DB02930	AGS	Adenosine 5'-[gamma-thio]triphosphate	1,210
DB02082	GNP	Phosphoaminophosphonic acid guanylate ester	935
DB04137	GTP	Guanosine-5'-Triphosphate	699
DB04444	ALF	Tetrafluoroaluminate Ion	281
DB03725	GCP	5'-Guanylylmethylenebisphosphonate	241
DB01812	A3P	Adenosine 3',5'-diphosphate	161
DB01864	GSP	5'-Guanosine-Diphosphate-Monothiophosphate	156
DB04005	UTP	Uridine 5'-triphosphate	135
DB02431	CTP	Cytidine-5'-Triphosphate	127
DB00131	AMP	Adenosine phosphate	122
DB01717	AP5	Bis(Adenosine)-5'-Pentaphosphate	116
DB02452	TTP	Thymidine 5'-triphosphate	111
DB03429	CDL	Tetrastearoyl cardiolipin	95
DB03435	UDP	Uridine-5'-Diphosphate	90
DB03222	DTP	dATP	83
DB01972	5GP	Guanosine-5'-Monophosphate	71
DB03909	ACP	Adenosine-5'-[Beta, Gamma-Methylene]Triphosphate	71

Most frequently bound compounds

PDB ligand	Name	Domains in contact
MGmetal	MAGNESIUM ION	9,035
ADP	ADENOSINE-5'-DIPHOSPHATE	5,001
ATP	ADENOSINE-5'-TRIPHOSPHATE	3,354
GDP	GUANOSINE-5'-DIPHOSPHATE	1,831
AGS	PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER	1,453
ANP	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER	1,063
GNP	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER	930
GTP	GUANOSINE-5'-TRIPHOSPHATE	667
CL	CHLORIDE ION	585
CAmetal	CALCIUM ION	461
BEF	BERYLLIUM TRIFLUORIDE ION	454
ZNmetal	ZINC ION	375
NAmetal	SODIUM ION	322
ALF	TETRAFLUOROALUMINATE ION	315
MNmetal	MANGANESE (II) ION	257
SF4	IRON/SULFUR CLUSTER	246
GCP	PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER	240
A3P	ADENOSINE-3'-5'-DIPHOSPHATE	168
GSP	5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE	156
AF3	ALUMINUM FLUORIDE	141