X-group (possible homology)

4044 Helical bundle domain in prismane-like proteins

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Ligands and drugs

737

Member domains

291

with ligand contacts (≤ 4 Å)

39.5% of members

158

with DrugDomain annotations

21.4% of members

with a DrugBank compound

7.3% 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)

—

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	5	5.8	0.86×	q = 0.84
Mixed metal/non-metal compounds	3	0.3	12×	not tested
Homogeneous non-metal compounds	9	2.6	3.53×	not tested
Organic nitrogen compounds	1	0.4	2.65×	not tested
Organic oxygen compounds	4	2.4	1.70×	not tested
Organoheterocyclic compounds	1	1.8	0.55×	not tested
Organic acids and derivatives	1	1.8	0.55×	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
DB14522	OH	Hydroxide ion	3
DB09157	CO2	Carbon dioxide	2
DB01826	NBN	N-Butyl Isocyanide	1
DB02078	PG5	Triglyme	1
DB02580	PG6	Pentaglyme	1
DB11588	CMO	Carbon monoxide	1

Most frequently bound compounds

PDB ligand	Name	Domains in contact
SF4	IRON/SULFUR CLUSTER	218
XCC	FE(4)-NI(1)-S(4) CLUSTER	50
XE	XENON	14
CL	CHLORIDE ION	8
CMO	CARBON MONOXIDE	8
CO2	CARBON DIOXIDE	8
NFS	FE(4)-NI(1)-S(5) CLUSTER	8
OH	HYDROXIDE ION	8
FEmetal	FE (III) ION	6
FES	FE2/S2 (INORGANIC) CLUSTER	6
MGmetal	MAGNESIUM ION	6
UW8	2-[3,8,8,12,12-pentakis(2-hydroxy-2-oxoethyl)-2,7,11-tris(oxidanylidene)-1,4,6,9,10,13-hexaoxa-5$l^{6}-titanaspiro[4.4^{5}.4^{5}]tridecan-3-yl]ethanoic acid	6
CYN	CYANIDE ION	5
BR	BROMIDE ION	4
MRD	(4R)-2-METHYLPENTANE-2,4-DIOL	4
CAmetal	CALCIUM ION	3
F	FLUORIDE ION	2
HOA	HYDROXYAMINE	2
Kmetal	POTASSIUM ION	2
NAmetal	SODIUM ION	2