X-group (possible homology)

232 Pentein

Open in classification tree →

Ligands and drugs

1,031

Member domains

189

with ligand contacts (≤ 4 Å)

18.3% of members

177

with DrugDomain annotations

17.2% of members

114

with a DrugBank compound

11.1% 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.

Proteins with classified ligands

Superclasses bound (of 23)

9.0

Superclasses per 20 proteins

broader than 80% 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
Homogeneous metal compounds	9	9.7	0.93×	q = 0.88
Nucleosides, nucleotides, and analogues	0	5.5	0	q = 8.0e-3
Organic acids and derivatives	10	3.1	3.28×	not tested
Organic nitrogen compounds	2	0.6	3.18×	not tested
Organosulfur compounds	1	0.4	2.46×	not tested
Benzenoids	3	1.4	2.08×	not tested
Homogeneous non-metal compounds	6	4.2	1.41×	not tested
Organoheterocyclic compounds	3	3.0	0.99×	not tested
Lipids and lipid-like molecules	1	2.2	0.46×	not tested
Organic oxygen compounds	1	3.9	0.26×	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
DB00125	ARG	Arginine	14
DB00155	—	Citrulline	11
DB07449	BFB	N-[(1S)-1-(aminocarbonyl)-4-(ethanimidoylamino)butyl]benzamide	6
DB00129	ORN	Ornithine	4
DB02501	SUG	N(2)-succinyl-L-arginine	4
DB03582	SUO	N~2~-Succinylornithine	4
DB00160	ALA	Alanine	3
DB00145	GLY	Glycine	2
DB03434	MPO	3-(N-morpholino)propanesulfonic acid	2
DB04422	HCS	Homocysteine	2
DB08838	AG2	Agmatine	2
DB00128	ASP	Aspartic acid	1
DB00130	GLN	L-Glutamine	1
DB00134	MET	Methionine	1
DB00151	CYS	Cysteine	1
DB00207	—	Azithromycin	1
DB00213	—	—	1
DB00736	—	—	1
DB00759	—	Tetracycline	1
DB01082	—	Streptomycin	1

Most frequently bound compounds

PDB ligand	Name	Domains in contact
CAmetal	CALCIUM ION	59
CL	CHLORIDE ION	28
Kmetal	POTASSIUM ION	19
NAmetal	SODIUM ION	15
ARG	ARGININE	14
MGmetal	MAGNESIUM ION	7
BFB	N-[(1S)-1-(AMINOCARBONYL)-4-(ETHANIMIDOYLAMINO)BUTYL]BENZAMIDE	6
NO6	S-[(pyridin-2-yl)methyl]-L-cysteine	6
CIR	CITRULLINE	5
ORN	L-ornithine	4
SUG	N~2~-(3-CARBOXYPROPANOYL)-L-ARGININE	4
SUO	N~2~-(3-CARBOXYPROPANOYL)-L-ORNITHINE	4
ZNmetal	ZINC ION	4
ALA	ALANINE	3
KQY	6-aminohexanamide	3
3YZ	[(3S,4R)-3-amino-4-hydroxypiperidin-1-yl]{2-[1-(cyclopropylmethyl)-1H-pyrrolo[2,3-b]pyridin-2-yl]-7-methoxy-1-methyl-1H-benzimidazol-5-yl}methanone	2
AG2	AGMATINE	2
AZI	AZIDE ION	2
D20	N~5~-{IMINO[(2-METHOXYETHYL)AMINO]METHYL}-L-ORNITHINE	2
GLY	GLYCINE	2