X-group (possible homology)

2496 SpoIIaa-like

Open in classification tree →

Ligands and drugs

1,509

Member domains

146

with ligand contacts (≤ 4 Å)

9.7% of members

136

with DrugDomain annotations

9.0% of members

with a DrugBank compound

5.7% 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)

9.6

Superclasses per 20 proteins

broader than 89% 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	6	11.1	0.54×	q = 0.06
Nucleosides, nucleotides, and analogues	2	6.3	0.32×	q = 0.09
Hydrocarbons	1	0.2	6.31×	not tested
Organosulfur compounds	2	0.5	4.29×	not tested
Lipids and lipid-like molecules	10	2.5	3.96×	not tested
Homogeneous non-metal compounds	11	4.9	2.25×	not tested
Benzenoids	2	1.7	1.21×	not tested
Organic oxygen compounds	2	4.5	0.44×	not tested
Organoheterocyclic compounds	1	3.5	0.29×	not tested
Organic acids and derivatives	1	3.5	0.28×	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
DB00163	VIV	Vitamin E	16
DB00171	ATP	ATP	5
DB16833	ADP	Adenosine disphosphate	5
DB03796	PLM	Palmitic Acid	3
DB14094	VTQ	Tocopherylquinone	3
DB18267	HEM	Ferroheme	3
DB02080	TRT	1-{2-[2-(2-Methoxyethoxy)Ethoxy]Ethoxy}-4-(1,1,3,3-Tetramethylbutyl)Benzene	2
DB04327	PEE	Phosphatidylethanolamine	2
DB09459	TLA	L-tartaric acid	2
DB11460	SQL	Squalene	2
DB14001	—	—	2
DB14002	—	—	2
DB16857	11A	Undecanoic acid	2

Most frequently bound compounds

PDB ligand	Name	Domains in contact
CL	CHLORIDE ION	18
VIV	(2R)-2,5,7,8-TETRAMETHYL-2-[(4R,8R)-4,8,12-TRIMETHYLTRIDECYL]CHROMAN-6-OL	13
B7N	(1R)-2-{[(S)-hydroxy{[(1S,2R,3R,4S,5S,6R)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}-1-[(octadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate	7
NAmetal	SODIUM ION	7
IOD	IODIDE ION	6
LBN	1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine	6
ATP	ADENOSINE-5'-TRIPHOSPHATE	5
PEV	(1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE	5
3PT	(2R)-3-{[(S)-hydroxy{[(1S,2R,3R,4S,5S,6S)-2,3,6-trihydroxy-4,5-bis(phosphonooxy)cyclohexyl]oxy}phosphoryl]oxy}propane-1,2-diyl dibutanoate	4
C14	TETRADECANE	4
D10	DECANE	4
NImetal	NICKEL (II) ION	4
OCT	N-OCTANE	4
POP	PYROPHOSPHATE 2-	4
PTY	PHOSPHATIDYLETHANOLAMINE	4
RET	RETINAL	4
6PL	(4S,7R)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSAN-1-AMINIUM 4-OXIDE	3
HEM	PROTOPORPHYRIN IX CONTAINING FE	3
MGmetal	MAGNESIUM ION	3
PBU	(2R)-3-{[(R)-HYDROXY{[(1R,2R,3S,4R,5R,6S)-2,3,6-TRIHYDROXY-4,5-BIS(PHOSPHONOOXY)CYCLOHEXYL]OXY}PHOSPHORYL]OXY}PROPANE-1,2-DIYL DIBUTANOATE	3