X-group (possible homology)

2002 TIM beta/alpha-barrel

Open in classification tree →

Ligands and drugs

65,243

Member domains

20,275

with ligand contacts (≤ 4 Å)

31.1% of members

19,876

with DrugDomain annotations

30.5% of members

14,233

with a DrugBank compound

21.8% 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.

2,135

Proteins with classified ligands

Superclasses bound (of 23)

8.7

Superclasses per 20 proteins

broader than 71% 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 oxygen compounds	739	419.2	1.76×	q < 0.0001
Organic acids and derivatives	424	325.7	1.30×	q < 0.0001
Homogeneous metal compounds	1,228	1,033.3	1.19×	q < 0.0001
Organoheterocyclic compounds	382	324.0	1.18×	q = 1.1e-3
Homogeneous non-metal compounds	517	453.1	1.14×	q = 1.6e-3
Benzenoids	151	153.9	0.98×	q = 0.88
Alkaloids and derivatives	7	7.2	0.97×	q = 1.00
Organosulfur compounds	41	43.3	0.95×	q = 0.87
Organic nitrogen compounds	54	67.2	0.80×	q = 0.14
Phenylpropanoids and polyketides	32	43.8	0.73×	q = 0.11
Nucleosides, nucleotides, and analogues	390	581.9	0.67×	q < 0.0001
Lipids and lipid-like molecules	111	234.4	0.47×	q < 0.0001
Hydrocarbons	5	14.7	0.34×	q = 0.01
Mixed metal/non-metal compounds	7	44.2	0.16×	q < 0.0001
Organohalogen compounds	0	6.0	0	q = 9.9e-3
Organic 1,3-dipolar compounds	8	1.8	4.54×	not tested
Organophosphorus compounds	1	0.7	1.40×	not tested
Miscellaneous inorganic compounds	1	1.6	0.64×	not tested
Hydrocarbon derivatives	1	1.8	0.55×	not tested
Organic salts	1	2.2	0.46×	not tested
Organometallic compounds	1	3.0	0.33×	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
DB03247	FMN	Flavin mononucleotide	1,161
DB00141	NAG	N-Acetylglucosamine	681
DB03461	NAP	Nicotinamide adenine dinucleotide phosphate	489
DB04566	IMP	Inosinic Acid	423
DB00119	PYR	Pyruvic acid	281
DB01819	PEP	Phosphoenolpyruvate	246
DB00114	PLP	Pyridoxal phosphate	200
DB02262	ORO	Orotic acid	183
DB14128	NAD	Nadide	180
DB02379	BGC	Beta-D-Glucose	172
DB00123	LYS	Lysine	164
DB03147	FAD	Flavin adenine dinucleotide	145
DB04326	13P	Dihydroxyacetone phosphate	125
DB02726	PGA	2-Phosphoglycolic Acid	122
DB02890	BMP	6-hydroxyuridine-5'-phosphate	114
DB00171	ATP	ATP	113
DB02338	NDP	NADPH	103
DB09459	TLA	L-tartaric acid	94
DB04137	GTP	Guanosine-5'-Triphosphate	88
DB04551	FBP	beta-D-fructofuranose 1,6-bisphosphate	83

Most frequently bound compounds

PDB ligand	Name	Domains in contact
MGmetal	MAGNESIUM ION	3,856
ZNmetal	ZINC ION	2,169
CL	CHLORIDE ION	1,748
CAmetal	CALCIUM ION	1,335
NAmetal	SODIUM ION	1,294
FMN	FLAVIN MONONUCLEOTIDE	1,157
Kmetal	POTASSIUM ION	900
MNmetal	MANGANESE (II) ION	892
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	650
NAP	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE	497
CAP	2-CARBOXYARABINITOL-1,5-DIPHOSPHATE	428
IMP	INOSINIC ACID	423
COmetal	COBALT (II) ION	299
PYR	PYRUVIC ACID	278
PEP	PHOSPHOENOLPYRUVATE	245
NImetal	NICKEL (II) ION	241
SF4	IRON/SULFUR CLUSTER	217
PLP	PYRIDOXAL-5'-PHOSPHATE	193
FEmetal	FE (III) ION	185
ORO	OROTIC ACID	183