X-group (possible homology)

300 Phospholipase D/nuclease

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Ligands and drugs

1,899

Member domains

338

with ligand contacts (≤ 4 Å)

17.8% of members

264

with DrugDomain annotations

13.9% of members

with a DrugBank compound

4.8% 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	6.3	0.80×	q = 0.66
Mixed metal/non-metal compounds	4	0.3	15×	not tested
Organic nitrogen compounds	1	0.4	2.45×	not tested
Benzenoids	2	0.9	2.13×	not tested
Homogeneous non-metal compounds	5	2.8	1.81×	not tested
Lipids and lipid-like molecules	2	1.4	1.40×	not tested
Organoheterocyclic compounds	2	2.0	1.01×	not tested
Organic acids and derivatives	2	2.0	1.01×	not tested
Organic oxygen compounds	2	2.6	0.78×	not tested
Nucleosides, nucleotides, and analogues	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
DB00127	SPM	Spermine	8
DB03434	MPO	3-(N-morpholino)propanesulfonic acid	8
DB00122	—	Choline	4
DB00171	ATP	ATP	4
DB14006	—	—	4
DB07898	HI5	(2R)-3-[(tetrahydroxyphosphoranyl)oxy]-1,2-propanediyl dibutanoate	2
DB08376	PD7	(2R)-3-(phosphonooxy)propane-1,2-diyl diheptanoate	2
DB09459	TLA	L-tartaric acid	2
DB14756	SRT	meso-Tartaric acid	2

Most frequently bound compounds

PDB ligand	Name	Domains in contact
VO4	VANADATE ION	36
OTS	4-(2S-AMINO-1-HYDROXYETHYL)PHENOL	20
CL	CHLORIDE ION	17
NAmetal	SODIUM ION	12
GHM	benzene-1,2,4-tricarboxylic acid	8
GJP	4-hydroxyquinoline-3-carboxylic acid	8
MPO	3[N-MORPHOLINO]PROPANE SULFONIC ACID	8
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	8
OTR	4-(2R-AMINO-1-HYDROXYETHYL)PHENOL	8
PO3	PHOSPHITE ION	8
SPM	SPERMINE	8
ATP	ADENOSINE-5'-TRIPHOSPHATE	6
IPD	D-MYO-INOSITOL-1-PHOSPHATE	6
VHY	(2R)-3-(phosphonooxy)propane-1,2-diyl dibutanoate	6
WO4	TUNGSTATE(VI)ION	6
ZNmetal	ZINC ION	6
IOD	IODIDE ION	5
A1AIM	(8M)-8-{4-(benzylcarbamoyl)-2-[(fluorosulfonyl)oxy]phenyl}-4-oxo-1,4-dihydroquinoline-3-carboxylic acid	4
GJS	4-hydroxybenzene-1,2-dicarboxylic acid	4
GM7	4-aminobenzene-1,2-dicarboxylic acid	4