X-group (possible homology)

2003 Rossmann-like

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Ligands and drugs

116,463

Member domains

35,113

with ligand contacts (≤ 4 Å)

30.1% of members

34,997

with DrugDomain annotations

30.0% of members

31,315

with a DrugBank compound

26.9% 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.

2,941

Proteins with classified ligands

Superclasses bound (of 23)

8.9

Superclasses per 20 proteins

broader than 78% 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	2,448	801.6	3.05×	q < 0.0001
Alkaloids and derivatives	17	9.9	1.72×	q = 0.05
Organohalogen compounds	11	8.3	1.33×	q = 0.36
Phenylpropanoids and polyketides	68	60.3	1.13×	q = 0.39
Benzenoids	221	212.0	1.04×	q = 0.59
Organic nitrogen compounds	90	92.5	0.97×	q = 0.88
Organic acids and derivatives	428	448.7	0.95×	q = 0.36
Homogeneous non-metal compounds	547	624.1	0.88×	q = 8.3e-4
Organosulfur compounds	52	59.7	0.87×	q = 0.42
Organoheterocyclic compounds	342	446.3	0.77×	q < 0.0001
Organic oxygen compounds	352	577.4	0.61×	q < 0.0001
Lipids and lipid-like molecules	169	322.9	0.52×	q < 0.0001
Homogeneous metal compounds	733	1,423.4	0.52×	q < 0.0001
Mixed metal/non-metal compounds	19	60.9	0.31×	q < 0.0001
Hydrocarbons	6	20.3	0.30×	q = 8.2e-4
Hydrocarbon derivatives	12	2.5	4.82×	not tested
Lignans, neolignans and related compounds	10	2.2	4.62×	not tested
Organic 1,3-dipolar compounds	5	2.4	2.06×	not tested
Organophosphorus compounds	1	1.0	1.02×	not tested
Miscellaneous inorganic compounds	1	2.2	0.46×	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
DB14128	NAD	NICOTINAMIDE-ADENINE-DINUCLEOTIDE	4,689
DB03147	FAD	FLAVIN-ADENINE DINUCLEOTIDE	4,382
DB04137	GTP	GUANOSINE-5'-TRIPHOSPHATE	4,258
DB04315	GDP	GUANOSINE-5'-DIPHOSPHATE	3,587
DB03461	NAP	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE	2,832
DB01752	SAH	S-ADENOSYL-L-HOMOCYSTEINE	1,632
DB02338	NDP	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE	1,431
DB00157	NAI	1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE	967
DB00114	PLP	PYRIDOXAL-5'-PHOSPHATE	757
DB00118	SAM	S-ADENOSYLMETHIONINE	596
DB16833	ADP	ADENOSINE-5'-DIPHOSPHATE	380
DB00640	ADN	ADENOSINE	357
DB01992	COA	COENZYME A	259
DB00171	ATP	ADENOSINE-5'-TRIPHOSPHATE	255
DB00142	GLU	GLUTAMIC ACID	181
DB03532	G2P	PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER	178
DB01229	TA1	TAXOL	158
DB01861	UPG	URIDINE-5'-DIPHOSPHATE-GLUCOSE	156
DB01910	SFG	SINEFUNGIN	154
DB02282	MTA	5'-DEOXY-5'-METHYLTHIOADENOSINE	127

Most frequently bound compounds

PDB ligand	Name	Domains in contact
MGmetal	MAGNESIUM ION	4,983
NAD	NICOTINAMIDE-ADENINE-DINUCLEOTIDE	4,644
FAD	FLAVIN-ADENINE DINUCLEOTIDE	4,381
GTP	GUANOSINE-5'-TRIPHOSPHATE	4,180
GDP	GUANOSINE-5'-DIPHOSPHATE	3,523
NAP	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE	2,891
CL	CHLORIDE ION	1,965
SAH	S-ADENOSYL-L-HOMOCYSTEINE	1,685
NDP	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE	1,385
NAmetal	SODIUM ION	1,329
CAmetal	CALCIUM ION	1,196
ZNmetal	ZINC ION	1,189
NAI	1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE	816
PLP	PYRIDOXAL-5'-PHOSPHATE	749
Kmetal	POTASSIUM ION	714
SAM	S-ADENOSYLMETHIONINE	615
ADP	ADENOSINE-5'-DIPHOSPHATE	373
ADN	ADENOSINE	357
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	349
SF4	IRON/SULFUR CLUSTER	281