X-group (possible homology)

304 Alpha-beta plaits

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Ligands and drugs

100,213

Member domains

14,005

with ligand contacts (≤ 4 Å)

14.0% of members

13,030

with DrugDomain annotations

13.0% of members

8,120

with a DrugBank compound

8.1% 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.

1,143

Proteins with classified ligands

Superclasses bound (of 23)

8.8

Superclasses per 20 proteins

broader than 75% 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
Nucleosides, nucleotides, and analogues	403	311.5	1.29×	q < 0.0001
Homogeneous non-metal compounds	304	242.6	1.25×	q < 0.0001
Organic acids and derivatives	187	174.4	1.07×	q = 0.37
Homogeneous metal compounds	574	553.2	1.04×	q = 0.29
Organosulfur compounds	23	23.2	0.99×	q = 1.00
Organic oxygen compounds	219	224.4	0.98×	q = 0.77
Benzenoids	68	82.4	0.82×	q = 0.15
Organoheterocyclic compounds	141	173.4	0.81×	q = 0.01
Phenylpropanoids and polyketides	19	23.4	0.81×	q = 0.48
Mixed metal/non-metal compounds	18	23.7	0.76×	q = 0.36
Organic nitrogen compounds	26	36.0	0.72×	q = 0.15
Lipids and lipid-like molecules	59	125.5	0.47×	q < 0.0001
Hydrocarbons	1	7.9	0.13×	q = 0.01
Organic 1,3-dipolar compounds	3	0.9	3.18×	not tested
Organometallic compounds	3	1.6	1.87×	not tested
Organohalogen compounds	5	3.2	1.56×	not tested
Alkaloids and derivatives	3	3.9	0.78×	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
DB18267	HEM	Ferroheme	609
DB03247	FMN	Flavin mononucleotide	455
DB03147	FAD	Flavin adenine dinucleotide	423
DB00171	ATP	ATP	243
DB16833	ADP	Adenosine disphosphate	236
DB00141	NAG	N-Acetylglucosamine	167
DB02832	SRM	Siroheme	166
DB03222	DTP	dATP	156
DB02181	DGT	2'-Deoxyguanosine-5'-Triphosphate	151
DB03258	DCP	2'-Deoxycytidine 5'-triphosphate	121
DB09110	COM	Coenzyme M	113
DB04137	GTP	Guanosine-5'-Triphosphate	110
DB02452	TTP	Thymidine 5'-triphosphate	106
DB00156	THR	Threonine	105
DB02596	APC	alpha,beta-Methyleneadenosine 5'-triphosphate	88
DB00131	AMP	Adenosine phosphate	87
DB02431	CTP	Cytidine-5'-Triphosphate	80
DB00123	LYS	Lysine	70
DB08864	T27	Rilpivirine	62
DB12529	NO2	Nitrite	61

Most frequently bound compounds

PDB ligand	Name	Domains in contact
MGmetal	MAGNESIUM ION	3,701
CL	CHLORIDE ION	998
CAmetal	CALCIUM ION	861
HEM	PROTOPORPHYRIN IX CONTAINING FE	610
ZNmetal	ZINC ION	547
FMN	FLAVIN MONONUCLEOTIDE	455
NAmetal	SODIUM ION	454
FAD	FLAVIN-ADENINE DINUCLEOTIDE	427
Kmetal	POTASSIUM ION	364
MNmetal	MANGANESE (II) ION	351
CAP	2-CARBOXYARABINITOL-1,5-DIPHOSPHATE	324
ATP	ADENOSINE-5'-TRIPHOSPHATE	244
ADP	ADENOSINE-5'-DIPHOSPHATE	229
OHX	osmium (III) hexammine	201
SRM	SIROHEME	166
DTP	2'-DEOXYADENOSINE 5'-TRIPHOSPHATE	156
DGT	2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE	149
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	148
FEmetal	FE (III) ION	137
DCP	2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE	124