X-group (possible homology)

188 Nuclear receptor ligand-binding domain

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Ligands and drugs

4,368

Member domains

3,163

with ligand contacts (≤ 4 Å)

72.4% of members

2,838

with DrugDomain annotations

65.0% of members

1,289

with a DrugBank compound

29.5% 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.

Proteins with classified ligands

Superclasses bound (of 23)

11.4

Superclasses per 20 proteins

broader than 99% 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
Benzenoids	43	6.2	6.94×	q < 0.0001
Lipids and lipid-like molecules	59	9.4	6.25×	q < 0.0001
Organoheterocyclic compounds	30	13.1	2.30×	q < 0.0001
Organic acids and derivatives	16	13.1	1.22×	q = 0.45
Homogeneous non-metal compounds	14	18.3	0.77×	q = 0.37
Organic oxygen compounds	12	16.9	0.71×	q = 0.29
Homogeneous metal compounds	17	41.6	0.41×	q < 0.0001
Nucleosides, nucleotides, and analogues	0	23.4	0	q < 0.0001
Organometallic compounds	3	0.1	25×	not tested
Lignans, neolignans and related compounds	1	0.1	16×	not tested
Miscellaneous inorganic compounds	1	0.1	16×	not tested
Alkaloids and derivatives	4	0.3	14×	not tested
Phenylpropanoids and polyketides	18	1.8	10×	not tested
Organohalogen compounds	2	0.2	8.28×	not tested
Organic nitrogen compounds	6	2.7	2.22×	not tested
Organosulfur compounds	3	1.7	1.72×	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
DB00783	EST	Estradiol	64
DB03338	B7G	Heptyl glucoside	57
DB02901	DHT	Stanolone	52
DB04468	OHT	Afimoxifene	38
DB00523	9CR	Alitretinoin	37
DB04349	PGO	(S)-propane-1,2-diol	35
DB01234	DEX	Dexamethasone	29
DB00755	REA	Tretinoin	22
DB00412	BRL	Rosiglitazone	21
DB07080	444	TO-901317	20
DB03047	EPH	L-Alpha-Phosphatidyl-Beta-Oleoyl-Gamma-Palmitoyl-Phosphatidylethanolamine	19
DB00136	VDX	Calcitriol	17
DB07863	GW9	2-chloro-5-nitro-N-phenylbenzamide	17
DB00255	DES	Diethylstilbestrol	14
DB00481	RAL	Raloxifene	14
DB03604	4HY	Tiratricol	14
DB00279	T3	Liothyronine	13
DB00396	STR	Progesterone	13
DB00421	SNL	Spironolactone	13
DB00624	TES	Testosterone	13

Most frequently bound compounds

PDB ligand	Name	Domains in contact
EST	ESTRADIOL	66
CL	CHLORIDE ION	60
B7G	heptyl beta-D-glucopyranoside	57
DHT	5-ALPHA-DIHYDROTESTOSTERONE	51
DEX	DEXAMETHASONE	46
OHT	4-HYDROXYTAMOXIFEN	36
PGO	S-1,2-PROPANEDIOL	35
NAmetal	SODIUM ION	33
9CR	(9cis)-retinoic acid	30
GW9	2-chloro-5-nitro-N-phenylbenzamide	22
444	N-(2,2,2-TRIFLUOROETHYL)-N-{4-[2,2,2-TRIFLUORO-1-HYDROXY-1-(TRIFLUOROMETHYL)ETHYL]PHENYL}BENZENESULFONAMIDE	19
EPH	L-ALPHA-PHOSPHATIDYL-BETA-OLEOYL-GAMMA-PALMITOYL-PHOSPHATIDYLETHANOLAMINE	19
EDK	(2~{S})-3-[4-[2-[methyl(pyridin-2-yl)amino]ethoxy]phenyl]-2-[[2-(phenylcarbonyl)phenyl]amino]propanoic acid	18
REA	RETINOIC ACID	18
CPS	3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE	17
VDX	5-{2-[1-(5-HYDROXY-1,5-DIMETHYL-HEXYL)-7A-METHYL-OCTAHYDRO-INDEN-4-YLIDENE]-ETHYLIDENE}-4-METHYLENE-CYCLOHEXANE-1,3-DIOL	17
BRL	2,4-THIAZOLIDIINEDIONE, 5-[[4-[2-(METHYL-2-PYRIDINYLAMINO)ETHOXY]PHENYL]METHYL]-(9CL)	16
Kmetal	POTASSIUM ION	16
KNA	nonanoic acid	15
4HY	[4-(4-HYDROXY-3-IODO-PHENOXY)-3,5-DIIODO-PHENYL]-ACETIC ACID	14