X-group (possible homology)

4 SH3

Open in classification tree →

Ligands and drugs

44,388

Member domains

6,657

with ligand contacts (≤ 4 Å)

15.0% of members

4,256

with DrugDomain annotations

9.6% of members

1,452

with a DrugBank compound

3.3% 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.

360

Proteins with classified ligands

Superclasses bound (of 23)

8.3

Superclasses per 20 proteins

broader than 62% 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
Organosulfur compounds	9	7.3	1.23×	q = 0.53
Mixed metal/non-metal compounds	9	7.5	1.21×	q = 0.65
Homogeneous metal compounds	205	174.2	1.18×	q = 2.9e-3
Homogeneous non-metal compounds	77	76.4	1.01×	q = 0.98
Organic nitrogen compounds	11	11.3	0.97×	q = 1.00
Lipids and lipid-like molecules	26	39.5	0.66×	q = 0.04
Benzenoids	17	26.0	0.66×	q = 0.10
Organoheterocyclic compounds	34	54.6	0.62×	q = 4.3e-3
Organic acids and derivatives	33	54.9	0.60×	q = 2.2e-3
Organic oxygen compounds	34	70.7	0.48×	q < 0.0001
Nucleosides, nucleotides, and analogues	23	98.1	0.23×	q < 0.0001
Phenylpropanoids and polyketides	0	7.4	0	q = 2.7e-3
Hydrocarbons	5	2.5	2.02×	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
DB03685	U5P	Uridine monophosphate	65
DB02745	URI	Uridine	41
DB03429	CDL	Tetrastearoyl cardiolipin	34
DB16833	ADP	Adenosine disphosphate	27
DB00141	NAG	N-Acetylglucosamine	25
DB00171	ATP	ATP	19
DB12010	—	Fostamatinib	17
DB09270	U10	Ubidecarenone	16
DB03345	BME	Mercaptoethanol	15
DB00536	GAI	Guanidine	12
DB09459	TLA	L-tartaric acid	12
DB01728	PEF	1,2-dihexadecanoyl-sn-glycero-3-phosphoethanolamine	11
DB00120	PHE	Phenylalanine	10
DB03309	NHE	N-cyclohexyltaurine	9
DB04079	HTO	Heptane-1,2,3-Triol	9
DB00145	GLY	Glycine	8
DB01643	TMP	Thymidine monophosphate	8
DB04349	PGO	(S)-propane-1,2-diol	8
DB14756	SRT	meso-Tartaric acid	8
DB00131	AMP	Adenosine phosphate	7

Most frequently bound compounds

PDB ligand	Name	Domains in contact
MGmetal	MAGNESIUM ION	3,079
ZNmetal	ZINC ION	574
OHX	osmium (III) hexammine	413
CL	CHLORIDE ION	359
UNX	UNKNOWN ATOM OR ION	323
NAmetal	SODIUM ION	285
Kmetal	POTASSIUM ION	237
LHG	1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE	76
A1L9F	N-(1-pyrenyl)maleimide	60
BAmetal	BARIUM ION	60
SRmetal	STRONTIUM ION	60
CAmetal	CALCIUM ION	56
CDmetal	CADMIUM ION	54
U5P	URIDINE-5'-MONOPHOSPHATE	49
SPD	SPERMIDINE	48
URI	URIDINE	41
COmetal	COBALT (II) ION	34
SPM	SPERMINE	34
NImetal	NICKEL (II) ION	32
MNmetal	MANGANESE (II) ION	31