X-group (possible homology)

213 Nat/Ivy

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Ligands and drugs

7,451

Member domains

2,287

with ligand contacts (≤ 4 Å)

30.7% of members

2,101

with DrugDomain annotations

28.2% of members

1,609

with a DrugBank compound

21.6% 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.

245

Proteins with classified ligands

Superclasses bound (of 23)

9.0

Superclasses per 20 proteins

broader than 80% 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
Lipids and lipid-like molecules	130	26.9	4.83×	q < 0.0001
Organic nitrogen compounds	14	7.7	1.82×	q = 0.06
Nucleosides, nucleotides, and analogues	105	66.8	1.57×	q < 0.0001
Homogeneous non-metal compounds	66	52.0	1.27×	q = 0.06
Organic acids and derivatives	43	37.4	1.15×	q = 0.40
Organic oxygen compounds	43	48.1	0.89×	q = 0.55
Benzenoids	12	17.7	0.68×	q = 0.28
Homogeneous metal compounds	62	118.6	0.52×	q < 0.0001
Organoheterocyclic compounds	19	37.2	0.51×	q = 1.6e-3
Phenylpropanoids and polyketides	1	5.0	0.20×	q = 0.11
Mixed metal/non-metal compounds	1	5.1	0.20×	q = 0.11
Organometallic compounds	2	0.3	5.81×	not tested
Miscellaneous inorganic compounds	1	0.2	5.55×	not tested
Organohalogen compounds	1	0.7	1.45×	not tested
Organosulfur compounds	4	5.0	0.81×	not tested
Hydrocarbons	1	1.7	0.59×	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
DB01992	COA	Coenzyme A	383
DB02180	MYA	Myristoyl-Coa	308
DB00127	SPM	Spermine	38
DB08231	MYR	Myristic acid	36
DB01694	TAR	D-tartaric acid	20
DB01421	PAR	Paromomycin	15
DB02663	PPQ	2-Amino-4-(Hydroxymethyl-Phosphinyl)Butanoic Acid	15
DB04075	NLG	N-Acetyl-L-Glutamate	15
DB07838	GN8	(Z)-3-BENZYL-5-(2-HYDROXY-3-NITROBENZYLIDENE)-2-THIOXOTHIAZOLIDIN-4-ONE	14
DB03699	SCA	Succinyl-Coenzyme A	13
DB00123	LYS	Lysine	12
DB02912	1VU	Propanoyl-CoA	12
DB04524	MLC	Malonyl-CoA	11
DB03435	UDP	Uridine-5'-Diphosphate	10
DB00141	NAG	N-Acetylglucosamine	9
DB03951	16G	N-acetyl-D-glucosamine-6-phosphate	9
DB14981	IHP	Phytic acid	9
DB00125	ARG	Arginine	8
DB00684	TOY	Tobramycin	8
DB02271	NHM	S-(2-oxo)pentadecylcoa	8

Most frequently bound compounds

PDB ligand	Name	Domains in contact
COA	COENZYME A	409
ACO	ACETYL COENZYME *A	371
MYA	TETRADECANOYL-COA	348
CL	CHLORIDE ION	285
MGmetal	MAGNESIUM ION	176
NHW	2-oxopentadecyl-CoA	124
NAmetal	SODIUM ION	95
CAmetal	CALCIUM ION	59
MYR	MYRISTIC ACID	54
SPM	SPERMINE	40
YNC	TETRADEC-13-YNOIC ACID - COA THIOESTER	30
ZNmetal	ZINC ION	29
CMC	CARBOXYMETHYL COENZYME *A	27
646	2,6-dichloro-4-(2-piperazin-1-ylpyridin-4-yl)-N-(1,3,5-trimethyl-1H-pyrazol-4-yl)benzenesulfonamide	24
PPQ	PHOSPHINOTHRICIN	23
TAR	D(-)-TARTARIC ACID	20
P6G	HEXAETHYLENE GLYCOL	18
UNX	UNKNOWN ATOM OR ION	17
NLG	N-ACETYL-L-GLUTAMATE	15
PAR	PAROMOMYCIN	15