X-group (possible homology)

1 cradle loop barrel

Open in classification tree →

Ligands and drugs

75,139

Member domains

14,865

with ligand contacts (≤ 4 Å)

19.8% of members

14,767

with DrugDomain annotations

19.7% of members

8,189

with a DrugBank compound

10.9% 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.

960

Proteins with classified ligands

Superclasses bound (of 23)

9.4

Superclasses per 20 proteins

broader than 87% 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	154	69.2	2.23×	q < 0.0001
Organic acids and derivatives	261	146.5	1.78×	q < 0.0001
Phenylpropanoids and polyketides	34	19.7	1.73×	q = 5.5e-3
Organosulfur compounds	32	19.5	1.64×	q = 0.01
Organic nitrogen compounds	46	30.2	1.52×	q = 1.0e-2
Organoheterocyclic compounds	155	145.7	1.06×	q = 0.47
Homogeneous non-metal compounds	198	203.7	0.97×	q = 0.76
Nucleosides, nucleotides, and analogues	245	261.7	0.94×	q = 0.30
Homogeneous metal compounds	423	464.6	0.91×	q = 0.01
Organic oxygen compounds	144	188.5	0.76×	q = 5.4e-4
Hydrocarbons	5	6.6	0.76×	q = 0.76
Mixed metal/non-metal compounds	14	19.9	0.70×	q = 0.28
Lipids and lipid-like molecules	26	105.4	0.25×	q < 0.0001
Organic salts	1	1.0	1.02×	not tested
Organohalogen compounds	2	2.7	0.74×	not tested
Organometallic compounds	1	1.4	0.74×	not tested
Alkaloids and derivatives	1	3.2	0.31×	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
DB03147	FAD	FLAVIN-ADENINE DINUCLEOTIDE	471
DB00141	NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	369
DB00114	PLP	PYRIDOXAL-5'-PHOSPHATE	173
DB03247	FMN	FLAVIN MONONUCLEOTIDE	162
DB01264	017	(3R,3AS,6AR)-HEXAHYDROFURO[2,3-B]FURAN-3-YL(1S,2R)-3-[[(4-AMINOPHENYL)SULFONYL](ISOBUTYL)AMINO]-1-BENZYL-2-HYDROXYPROPYLCARBAMATE	161
DB02078	PG5	1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE	98
DB03461	NAP	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE	96
DB00171	ATP	ADENOSINE-5'-TRIPHOSPHATE	71
DB01232	ROC	(2S)-N-[(2S,3R)-4-[(2S,3S,4aS,8aS)-3-(tert-butylcarbamoyl)-3,4,4a,5,6,7,8,8a-octahydro-1H-isoquinolin-2-yl]-3-hydroxy-1-phenyl-butan-2-yl]-2-(quinolin-2-ylcarbonylamino)butanediamide	65
DB09459	TLA	L(+)-TARTARIC ACID	62
DB03345	BME	BETA-MERCAPTOETHANOL	59
DB00701	478	{3-[(4-AMINO-BENZENESULFONYL)-ISOBUTYL-AMINO]-1-BENZYL-2-HYDROXY-PROPYL}-CARBAMIC ACID TETRAHYDRO-FURAN-3-YL ESTER	54
DB16833	ADP	ADENOSINE-5'-DIPHOSPHATE	43
DB00224	MK1	N-[2(R)-HYDROXY-1(S)-INDANYL]-5-[(2(S)-TERTIARYBUTYLAMINOCARBONYL)-4(3-PYRIDYLMETHYL)PIPERAZINO]-4(S)-HYDROXY-2(R)-PHENYLMETHYLPENTANAMIDE	36
DB06841	0G6	D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide	35
DB00503	RIT	RITONAVIR	33
DB02313	AG7	4-{2-(4-FLUORO-BENZYL)-6-METHYL-5-[(5-METHYL-ISOXAZOLE-3-CARBONYL)-AMINO]-4-OXO-HEPTANOYLAMINO}-5-(2-OXO-PYRROLIDIN-3-YL)-PENTANOIC ACID ETHYL ESTER	32
DB03913	F42	COENZYME F420	31
DB18834	7YY	6-[(6-chloranyl-2-methyl-indazol-5-yl)amino]-3-[(1-methyl-1,2,4-triazol-3-yl)methyl]-1-[[2,4,5-tris(fluoranyl)phenyl]methyl]-1,3,5-triazine-2,4-dione	31
DB01694	TAR	D(-)-TARTARIC ACID	29

Most frequently bound compounds

PDB ligand	Name	Domains in contact
MGmetal	MAGNESIUM ION	2,171
CL	CHLORIDE ION	1,219
CAmetal	CALCIUM ION	1,117
NAmetal	SODIUM ION	632
FAD	FLAVIN-ADENINE DINUCLEOTIDE	467
ZNmetal	ZINC ION	433
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	335
MNmetal	MANGANESE (II) ION	237
Kmetal	POTASSIUM ION	190
IOD	IODIDE ION	174
MGD	2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE	162
017	(3R,3AS,6AR)-HEXAHYDROFURO[2,3-B]FURAN-3-YL(1S,2R)-3-[[(4-AMINOPHENYL)SULFONYL](ISOBUTYL)AMINO]-1-BENZYL-2-HYDROXYPROPYLCARBAMATE	161
FMN	FLAVIN MONONUCLEOTIDE	156
PLP	PYRIDOXAL-5'-PHOSPHATE	145
BEN	BENZAMIDINE	144
OHX	osmium (III) hexammine	130
PG5	1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE	98
NAP	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE	91
U1H	[4-(trifluoromethyl)phenyl]methanamine	78
UNX	UNKNOWN ATOM OR ION	77