X-group (possible homology)

220 PH domain-like

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Ligands and drugs

10,841

Member domains

645

with ligand contacts (≤ 4 Å)

5.9% of members

541

with DrugDomain annotations

5.0% of members

408

with a DrugBank compound

3.8% 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)

7.7

Superclasses per 20 proteins

broader than 51% 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
Organic oxygen compounds	34	13.7	2.47×	q < 0.0001
Homogeneous non-metal compounds	19	14.9	1.28×	q = 0.31
Lipids and lipid-like molecules	8	7.7	1.04×	q = 0.89
Organic acids and derivatives	9	10.7	0.84×	q = 0.80
Benzenoids	3	5.1	0.59×	q = 0.57
Homogeneous metal compounds	14	33.9	0.41×	q < 0.0001
Organoheterocyclic compounds	4	10.6	0.38×	q = 0.05
Nucleosides, nucleotides, and analogues	1	19.1	0.05×	q < 0.0001
Organosulfur compounds	2	1.4	1.41×	not tested
Organic nitrogen compounds	3	2.2	1.36×	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	36
DB01863	4IP	Inositol 1,3,4,5-Tetrakisphosphate	29
DB04481	MRY	Erythritol	12
DB03401	I3P	1D-myo-inositol 1,4,5-trisphosphate	11
DB12010	—	Fostamatinib	5
DB00120	PHE	Phenylalanine	4
DB02082	GNP	Phosphoaminophosphonic acid guanylate ester	4
DB14981	IHP	Phytic acid	4
DB02175	MLA	Malonic acid	3
DB03344	I5P	Inositol-(1,3,4,5,6)-Pentakisphosphate	3
DB04522	SEP	Dexfosfoserine	3
DB02676	B3P	2-[3-(2-Hydroxy-1,1-Dihydroxymethyl-Ethylamino)-Propylamino]-2-Hydroxymethyl-Propane-1,3-Diol	2
DB03345	BME	Mercaptoethanol	2
DB15035	—	—	2
DB00122	—	Choline	1
DB00133	SER	Serine	1
DB00142	GLU	Glutamic acid	1
DB00144	—	Phosphatidyl serine	1
DB00482	—	Celecoxib	1
DB00619	—	Imatinib	1

Most frequently bound compounds

PDB ligand	Name	Domains in contact
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	99
MGmetal	MAGNESIUM ION	45
ZNmetal	ZINC ION	40
CL	CHLORIDE ION	34
4IP	INOSITOL-(1,3,4,5)-TETRAKISPHOSPHATE	33
UNX	UNKNOWN ATOM OR ION	17
MRY	MESO-ERYTHRITOL	13
NAmetal	SODIUM ION	10
I3P	D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE	9
BR	BROMIDE ION	8
CAmetal	CALCIUM ION	8
4PT	(2R)-3-{[(S)-{[(2S,3R,5S,6S)-2,6-DIHYDROXY-3,4,5-TRIS(PHOSPHONOOXY)CYCLOHEXYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-2-(1-HYDROXYBUTOXY)PROPYL BUTYRATE	6
CSmetal	CESIUM ION	5
8SE	(3~{S},7~{R},10~{R},13~{S})-4-[[(3~{S},7~{R},10~{R},13~{S})-4-[(2~{S})-2-acetamido-3-(2-chlorophenyl)propanoyl]-2-oxidanylidene-1,4-diazatricyclo[8.3.0.0^{3,7}]tridec-8-en-13-yl]carbonyl]-2-oxidanylidene-1,4-diazatricyclo[8.3.0.0^{3,7}]tridec-8-ene-13-carboxylic acid	4
A1JIA	(6~{S})-6-(5-bromanylthiophen-2-yl)-6,7-dihydro-1-benzofuran-3-carboxylic acid	4
IHP	INOSITOL HEXAKISPHOSPHATE	4
NImetal	NICKEL (II) ION	4
NXT	4,5,6,7-tetrahydro-1-benzofuran-3-carboxylic acid	4
NYQ	5-bromanyl-1,3-dihydroindol-2-one	4
PHE	PHENYLALANINE	4