X-group (possible homology)

11 Immunoglobulin-like beta-sandwich

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Ligands and drugs

170,854

Member domains

27,812

with ligand contacts (≤ 4 Å)

16.3% of members

18,274

with DrugDomain annotations

10.7% of members

11,653

with a DrugBank compound

6.8% 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.

1,569

Proteins with classified ligands

Superclasses bound (of 23)

8.0

Superclasses per 20 proteins

broader 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
Alkaloids and derivatives	18	5.3	3.41×	q < 0.0001
Organic oxygen compounds	694	308.1	2.25×	q < 0.0001
Organic nitrogen compounds	69	49.4	1.40×	q = 0.01
Homogeneous non-metal compounds	379	333.0	1.14×	q = 8.8e-3
Homogeneous metal compounds	784	759.4	1.03×	q = 0.28
Organosulfur compounds	32	31.8	1.00×	q = 0.96
Benzenoids	83	113.1	0.73×	q = 5.3e-3
Lipids and lipid-like molecules	126	172.3	0.73×	q = 2.8e-4
Organic acids and derivatives	153	239.4	0.64×	q < 0.0001
Phenylpropanoids and polyketides	18	32.2	0.56×	q = 0.02
Hydrocarbons	6	10.8	0.56×	q = 0.22
Organoheterocyclic compounds	93	238.1	0.39×	q < 0.0001
Mixed metal/non-metal compounds	9	32.5	0.28×	q < 0.0001
Nucleosides, nucleotides, and analogues	21	427.6	0.05×	q < 0.0001
Organic salts	3	1.6	1.86×	not tested
Organohalogen compounds	8	4.4	1.81×	not tested
Organometallic compounds	3	2.2	1.36×	not tested
Lignans, neolignans and related compounds	1	1.2	0.87×	not tested
Miscellaneous inorganic compounds	1	1.2	0.87×	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	2-acetamido-2-deoxy-beta-D-glucopyranose	3,668
DB02530	ABU	GAMMA-AMINO-BUTANOIC ACID	185
DB00145	GLY	GLYCINE	159
DB03345	BME	BETA-MERCAPTOETHANOL	146
DB09459	TLA	L(+)-TARTARIC ACID	113
DB18267	HEM	PROTOPORPHYRIN IX CONTAINING FE	99
DB02777	PLC	DIUNDECYL PHOSPHATIDYL CHOLINE	92
DB00184	NCT	(S)-3-(1-METHYLPYRROLIDIN-2-YL)PYRIDINE	67
DB08231	MYR	MYRISTIC ACID	67
DB03946	DHB	3,4-DIHYDROXYBENZOIC ACID	62
DB15954	SY9	STRYCHNINE	60
DB00171	ATP	ADENOSINE-5'-TRIPHOSPHATE	56
DB01593	—	—	54
DB14487	—	—	54
DB04473	FUC	alpha-L-fucopyranose	53
DB00898	—	—	52
DB14533	—	—	42
DB00151	CYS	CYSTEINE	41
DB05137	L0B	Alpha-Lobeline	38
DB12010	—	—	38

Most frequently bound compounds

PDB ligand	Name	Domains in contact
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	4,330
CL	CHLORIDE ION	2,192
CAmetal	CALCIUM ION	2,054
ZNmetal	ZINC ION	2,031
NAmetal	SODIUM ION	1,398
CUmetal	COPPER (II) ION	847
MGmetal	MAGNESIUM ION	675
FEmetal	FE (III) ION	310
PLC	DIUNDECYL PHOSPHATIDYL CHOLINE	281
IOD	IODIDE ION	251
CDmetal	CADMIUM ION	250
MAN	alpha-D-mannopyranose	211
ABU	GAMMA-AMINO-BUTANOIC ACID	182
GLY	GLYCINE	176
Kmetal	POTASSIUM ION	172
NImetal	NICKEL (II) ION	163
BR	BROMIDE ION	158
BME	BETA-MERCAPTOETHANOL	150
TLA	L(+)-TARTARIC ACID	125
CU1metal	COPPER (I) ION	122