X-group (possible homology)

221 beta-Grasp

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Ligands and drugs

30,416

Member domains

5,461

with ligand contacts (≤ 4 Å)

18.0% of members

4,355

with DrugDomain annotations

14.3% of members

1,908

with a DrugBank compound

6.3% 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.

355

Proteins with classified ligands

Superclasses bound (of 23)

9.2

Superclasses per 20 proteins

broader than 83% 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
Organic nitrogen compounds	25	11.2	2.24×	q = 5.5e-4
Organosulfur compounds	11	7.2	1.53×	q = 0.24
Nucleosides, nucleotides, and analogues	136	96.8	1.41×	q < 0.0001
Homogeneous non-metal compounds	93	75.3	1.23×	q = 0.05
Homogeneous metal compounds	194	171.8	1.13×	q = 0.03
Mixed metal/non-metal compounds	7	7.4	0.95×	q = 1.00
Benzenoids	23	25.6	0.90×	q = 0.75
Organoheterocyclic compounds	36	53.9	0.67×	q = 0.01
Phenylpropanoids and polyketides	4	7.3	0.55×	q = 0.34
Organic oxygen compounds	34	69.7	0.49×	q < 0.0001
Organic acids and derivatives	26	54.2	0.48×	q < 0.0001
Lipids and lipid-like molecules	14	39.0	0.36×	q < 0.0001
Miscellaneous inorganic compounds	2	0.3	7.66×	not tested
Organohalogen compounds	6	1.0	6.02×	not tested
Organometallic compounds	1	0.5	2.01×	not tested
Hydrocarbons	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
DB03147	FAD	Flavin adenine dinucleotide	286
DB00157	NAI	NADH	107
DB03247	FMN	Flavin mononucleotide	39
DB08217	MTN	S-[(1-Hydroxy-2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrol-3-yl)methyl] methanesulfonothioate	31
DB00131	AMP	Adenosine phosphate	29
DB00171	ATP	ATP	27
DB14128	NAD	Nadide	26
DB02023	8OG	8-oxo-dGMP	24
DB00115	CNC	Cyanocobalamin	13
DB12010	—	Fostamatinib	12
DB01799	EIP	4-Hydroxy-3-Methyl Butyl Diphosphate	10
DB03317	HEC	Ferroheme C	10
DB02059	AR6	Adenosine-5-Diphosphoribose	9
DB04464	—	N-Formylmethionine	9
DB02082	GNP	Phosphoaminophosphonic acid guanylate ester	8
DB03723	TRH	2'-Deoxy-thymidine-beta-L-rhamnose	8
DB02175	MLA	Malonic acid	7
DB03983	MTQ	{[2-Amino-4-oxo-6,7-di(sulfanyl-κS)-3,5,5a,8,9a,10-hexahydro-4H-pyrano[3,2-g]pteridin-8-yl]methyl dihydrogenato(2-) phosphate}(dioxo)sulfanylmolybdenum	7
DB04137	GTP	Guanosine-5'-Triphosphate	7
DB04315	GDP	Guanosine-5'-Diphosphate	7

Most frequently bound compounds

PDB ligand	Name	Domains in contact
MGmetal	MAGNESIUM ION	1,275
FES	FE2/S2 (INORGANIC) CLUSTER	1,094
ZNmetal	ZINC ION	568
SF4	IRON/SULFUR CLUSTER	360
CL	CHLORIDE ION	305
FAD	FLAVIN-ADENINE DINUCLEOTIDE	191
NAmetal	SODIUM ION	167
MNmetal	MANGANESE (II) ION	120
NAI	1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE	102
AYE	prop-2-en-1-amine	80
OHX	osmium (III) hexammine	77
CAmetal	CALCIUM ION	73
APR	ADENOSINE-5-DIPHOSPHORIBOSE	63
AMP	ADENOSINE MONOPHOSPHATE	54
8DG	8-OXO-2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE	47
CDmetal	CADMIUM ION	45
NAD	NICOTINAMIDE-ADENINE-DINUCLEOTIDE	39
ATP	ADENOSINE-5'-TRIPHOSPHATE	37
Kmetal	POTASSIUM ION	37
UNX	UNKNOWN ATOM OR ION	36