X-group (possible homology)

375 Rubredoxin-like

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Ligands and drugs

27,444

Member domains

6,571

with ligand contacts (≤ 4 Å)

23.9% of members

5,935

with DrugDomain annotations

21.6% of members

549

with a DrugBank compound

2.0% 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.

543

Proteins with classified ligands

Superclasses bound (of 23)

5.1

Superclasses per 20 proteins

narrower than 81% 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
Homogeneous metal compounds	525	262.8	2.00×	q < 0.0001
Organic nitrogen compounds	12	17.1	0.70×	q = 0.34
Mixed metal/non-metal compounds	7	11.2	0.62×	q = 0.30
Organosulfur compounds	5	11.0	0.45×	q = 0.10
Phenylpropanoids and polyketides	5	11.1	0.45×	q = 0.10
Nucleosides, nucleotides, and analogues	56	148.0	0.38×	q < 0.0001
Organoheterocyclic compounds	18	82.4	0.22×	q < 0.0001
Benzenoids	8	39.1	0.20×	q < 0.0001
Organic acids and derivatives	14	82.8	0.17×	q < 0.0001
Lipids and lipid-like molecules	8	59.6	0.13×	q < 0.0001
Homogeneous non-metal compounds	12	115.2	0.10×	q < 0.0001
Organic oxygen compounds	10	106.6	0.09×	q < 0.0001
Organic 1,3-dipolar compounds	1	0.5	2.23×	not tested
Alkaloids and derivatives	3	1.8	1.64×	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
DB01717	AP5	Bis(Adenosine)-5'-Pentaphosphate	80
DB02659	CHD	Cholic Acid	56
DB16833	ADP	Adenosine disphosphate	33
DB00171	ATP	ATP	24
DB00131	AMP	Adenosine phosphate	17
DB17057	SR7	SRT-1720	12
DB03566	SPD	Spermidine	9
DB03725	GCP	5'-Guanylylmethylenebisphosphonate	7
DB14128	NAD	Nadide	7
DB00118	SAM	Ademetionine	6
DB00123	LYS	Lysine	6
DB00149	LEU	Leucine	6
DB00127	SPM	Spermine	5
DB03345	BME	Mercaptoethanol	5
DB03478	OAD	2'-O-Acetyl Adenosine-5-Diphosphoribose	5
DB04381	CRD	Crotonaldehyde	5
DB00242	—	Cladribine	4
DB02916	LMS	[(2r,3s,4r,5r)-5-(6-Amino-9h-Purin-9-Yl)-3,4-Dihydroxytetrahydro-2-Furanyl]Methyl Sulfamate	3
DB03103	TYD	Thymidine-5'- Diphosphate	3
DB03403	C	Cytidine-5'-Monophosphate	3

Most frequently bound compounds

PDB ligand	Name	Domains in contact
ZNmetal	ZINC ION	5,551
MGmetal	MAGNESIUM ION	1,247
CDmetal	CADMIUM ION	210
OHX	osmium (III) hexammine	148
FEmetal	FE (III) ION	128
CL	CHLORIDE ION	87
AP5	BIS(ADENOSINE)-5'-PENTAPHOSPHATE	80
PEK	(1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE	78
NAmetal	SODIUM ION	64
SRmetal	STRONTIUM ION	60
ADP	ADENOSINE-5'-DIPHOSPHATE	35
Kmetal	POTASSIUM ION	34
FE2metal	FE (II) ION	24
SPD	SPERMIDINE	19
ATP	ADENOSINE-5'-TRIPHOSPHATE	18
UNX	UNKNOWN ATOM OR ION	15
AMP	ADENOSINE MONOPHOSPHATE	14
3HE	4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione	12
CAmetal	CALCIUM ION	12
8L9	5-[[3,5-bis(chloranyl)phenyl]sulfonylamino]-2-[(5-bromanyl-4-fluoranyl-2-methyl-phenyl)sulfamoyl]benzoic acid	9