X-group (possible homology)

5095 N-terminal beta-sandwich domain in anthrax protective antigen

Open in classification tree →

Ligands and drugs

297

Member domains

116

with ligand contacts (≤ 4 Å)

39.1% of members

with DrugDomain annotations

26.3% of members

with a DrugBank compound

14.5% 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)

—

Superclasses per 20 proteins

fewer than 20 proteins: too few to compare at equal depth

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	14	8.2	1.70×	q = 0.01
Organic oxygen compounds	9	3.3	2.70×	not tested
Homogeneous non-metal compounds	3	3.6	0.83×	not tested
Organoheterocyclic compounds	1	2.6	0.39×	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
DB00141	NAG	N-Acetylglucosamine	6
DB02379	BGC	Beta-D-Glucose	5
DB03740	NDG	N-acetyl-alpha-D-glucosamine	5
DB03283	FUL	beta-L-fucose	1
DB03389	XYS	alpha-D-Xylopyranose	1
DB04286	RIP	beta-D-Ribopyranose	1
DB04473	FUC	alpha-L-fucose	1
DB13178	INS	Inositol	1

Most frequently bound compounds

PDB ligand	Name	Domains in contact
CAmetal	CALCIUM ION	95
CL	CHLORIDE ION	19
NAmetal	SODIUM ION	18
GDmetal	GADOLINIUM ATOM	8
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	6
NDG	2-acetamido-2-deoxy-alpha-D-glucopyranose	5
BGC	beta-D-glucopyranose	3
MAN	alpha-D-mannopyranose	3
BMA	beta-D-mannopyranose	2
MGmetal	MAGNESIUM ION	2
3MG	3-O-methyl-beta-D-glucopyranose	1
ARA	alpha-L-arabinopyranose	1
FUC	alpha-L-fucopyranose	1
FUL	beta-L-fucopyranose	1
GAL	beta-D-galactopyranose	1
GLC	alpha-D-glucopyranose	1
GYP	methyl alpha-D-glucopyranoside	1
INS	1,2,3,4,5,6-HEXAHYDROXY-CYCLOHEXANE	1
PXN	(2S)-1-[3-{[(2R)-2-hydroxypropyl]oxy}-2,2-bis({[(2R)-2-hydroxypropyl]oxy}methyl)propoxy]propan-2-ol	1
RIP	beta-D-ribopyranose	1