X-group (possible homology)

328 IF3-like

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Ligands and drugs

5,713

Member domains

724

with ligand contacts (≤ 4 Å)

12.7% of members

667

with DrugDomain annotations

11.7% of members

383

with a DrugBank compound

6.7% 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)

7.0

Superclasses per 20 proteins

narrower than 58% 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 acids and derivatives	19	7.9	2.40×	q = 4.2e-4
Nucleosides, nucleotides, and analogues	22	14.2	1.55×	q = 0.03
Homogeneous non-metal compounds	14	11.0	1.27×	q = 0.39
Homogeneous metal compounds	26	25.2	1.03×	q = 0.93
Organic oxygen compounds	8	10.2	0.78×	q = 0.68
Organoheterocyclic compounds	2	7.9	0.25×	q = 0.03
Lipids and lipid-like molecules	0	5.7	0	q = 0.01
Organosulfur compounds	1	1.1	0.95×	not tested
Organic nitrogen compounds	1	1.6	0.61×	not tested
Benzenoids	2	3.8	0.53×	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
DB04328	S3P	Shikimate-3-Phosphate	66
DB03397	UD1	Uridine-Diphosphate-N-Acetylglucosamine	60
DB04539	GPJ	Glyphosate	33
DB01733	0V5	L-Phospholactate	32
DB04174	UDA	3'-1-carboxy-1-phosphonooxy-ethoxy-uridine-diphosphate-N-acetylglucosamine	32
DB01819	PEP	Phosphoenolpyruvate	14
DB00171	ATP	ATP	11
DB01861	UPG	Uridine diphosphate glucose	10
DB03435	UDP	Uridine-5'-Diphosphate	10
DB01879	TAV	(S)-2-{Methyl-[2-(Naphthalene-2-Sulfonylamino)-5-(Naphthalene-2-Sulfonyloxy)-Benzoyl]-Amino}-Succinicacid	8
DB02995	HAI	Cyclohexylammonium Ion	8
DB00131	AMP	Adenosine phosphate	7
DB03345	BME	Mercaptoethanol	7
DB00125	ARG	Arginine	4
DB03116	SKP	5-(1-Carboxy-1-Phosphonooxy-Ethoxyl)-Shikimate-3-Phosphate	4
DB01694	TAR	D-tartaric acid	3
DB00640	ADN	Adenosine	2
DB02196	UD2	Uridine-Diphosphate-N-Acetylgalactosamine	2
DB04005	UTP	Uridine 5'-triphosphate	2
DB00142	—	Glutamic acid	1

Most frequently bound compounds

PDB ligand	Name	Domains in contact
ZNmetal	ZINC ION	105
S3P	SHIKIMATE-3-PHOSPHATE	85
EPU	URIDINE-DIPHOSPHATE-2(N-ACETYLGLUCOSAMINYL) BUTYRIC ACID	78
UD1	URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE	60
EPZ	(2R)-2-{[(2R,3R,4R,5S,6R)-3-(acetylamino)-2-{[(S)-{[(R)-{[(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}-5-hydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-4-yl]oxy}propanoic acid	58
GPJ	GLYPHOSATE	55
CL	CHLORIDE ION	50
MGmetal	MAGNESIUM ION	36
0V5	(2R)-2-(phosphonooxy)propanoic acid	32
UDA	3'-1-CARBOXY-1-PHOSPHONOOXY-ETHOXY-URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE	32
FFQ	[(1R)-1-hydroxypropyl]phosphonic acid	30
NAmetal	SODIUM ION	26
PO3	PHOSPHITE ION	24
Kmetal	POTASSIUM ION	17
SKM	(3R,4S,5R)-3,4,5-TRIHYDROXYCYCLOHEX-1-ENE-1-CARBOXYLIC ACID	16
PEP	PHOSPHOENOLPYRUVATE	14
CAmetal	CALCIUM ION	10
UDP	URIDINE-5'-DIPHOSPHATE	10
HAI	CYCLOHEXYLAMMONIUM ION	9
UPG	URIDINE-5'-DIPHOSPHATE-GLUCOSE	9