X-group (possible homology)

2488 alpha/beta knot

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Ligands and drugs

2,811

Member domains

387

with ligand contacts (≤ 4 Å)

13.8% of members

355

with DrugDomain annotations

12.6% of members

233

with a DrugBank compound

8.3% 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.

Proteins with classified ligands

Superclasses bound (of 23)

6.6

Superclasses per 20 proteins

narrower than 66% 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	52	15.3	3.41×	q < 0.0001
Homogeneous non-metal compounds	8	11.9	0.67×	q = 0.33
Organoheterocyclic compounds	5	8.5	0.59×	q = 0.34
Organic acids and derivatives	3	8.5	0.35×	q = 0.06
Homogeneous metal compounds	7	27.1	0.26×	q < 0.0001
Organic oxygen compounds	2	11.0	0.18×	q = 2.6e-3
Lipids and lipid-like molecules	0	6.2	0	q = 5.0e-3
Organic 1,3-dipolar compounds	1	0.1	22×	not tested
Organosulfur compounds	1	1.1	0.88×	not tested
Benzenoids	3	4.0	0.74×	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
DB01752	SAH	S-adenosyl-L-homocysteine	70
DB00118	SAM	Ademetionine	62
DB01910	SFG	Sinefungin	21
DB02282	MTA	5'-S-methyl-5'-thioadenosine	8
DB00640	ADN	Adenosine	5
DB00173	ADE	Adenine	2
DB04130	5OB	5-Methoxybenzimidazole	2
DB04349	PGO	(S)-propane-1,2-diol	2
DB00135	TYR	Tyrosine	1
DB03345	BME	Mercaptoethanol	1

Most frequently bound compounds

PDB ligand	Name	Domains in contact
SAH	S-ADENOSYL-L-HOMOCYSTEINE	88
SAM	S-ADENOSYLMETHIONINE	67
CL	CHLORIDE ION	26
SFG	SINEFUNGIN	22
MTA	5'-DEOXY-5'-METHYLTHIOADENOSINE	9
ADN	ADENOSINE	6
MGmetal	MAGNESIUM ION	6
UNX	UNKNOWN ATOM OR ION	4
21X	N-[4-(aminomethyl)benzyl]-4-oxo-3,4-dihydrothieno[2,3-d]pyrimidine-5-carboxamide	3
9D0	N-({4-[(octylamino)methyl]phenyl}methyl)-4-oxo-3,4-dihydrothieno[2,3-d]pyrimidine-5-carboxamide	3
BWR	~{N}-[[4-[(4-azanylpiperidin-1-yl)methyl]phenyl]methyl]-4-oxidanylidene-3~{H}-thieno[2,3-d]pyrimidine-5-carboxamide	3
EEM	[(3S)-3-amino-4-hydroxy-4-oxo-butyl]-[[(2S,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl]-methyl-selanium	3
NAmetal	SODIUM ION	3
15P	POLYETHYLENE GLYCOL (N=34)	2
21W	N-(4-{[(1H-imidazol-2-ylmethyl)amino]methyl}benzyl)-4-oxo-3,4-dihydrothieno[2,3-d]pyrimidine-5-carboxamide	2
5OB	5-METHOXYBENZIMIDAZOLE	2
6GU	6-chloroguanine	2
6SD	3-(4-methoxyphenyl)-1~{H}-pyrazol-5-amine	2
97T	2-(1,2-oxazol-5-yl)phenol	2
9D3	N-({4-[(diethylamino)methyl]phenyl}methyl)-4-oxo-3,4-dihydrothieno[2,3-d]pyrimidine-5-carboxamide	2