X-group (possible homology)

4019 alpha-helical domain in beta-lactamase/transpeptidase-like proteins

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Ligands and drugs

4,174

Member domains

2,925

with ligand contacts (≤ 4 Å)

70.1% of members

2,621

with DrugDomain annotations

62.8% of members

1,381

with a DrugBank compound

33.1% 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.

220

Proteins with classified ligands

Superclasses bound (of 23)

8.4

Superclasses per 20 proteins

broader than 65% 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	143	33.6	4.26×	q < 0.0001
Benzenoids	41	15.9	2.58×	q < 0.0001
Organoheterocyclic compounds	70	33.4	2.10×	q < 0.0001
Organic nitrogen compounds	12	6.9	1.73×	q = 0.12
Homogeneous non-metal compounds	63	46.7	1.35×	q = 0.02
Organic oxygen compounds	34	43.2	0.79×	q = 0.18
Homogeneous metal compounds	40	106.5	0.38×	q < 0.0001
Lipids and lipid-like molecules	8	24.2	0.33×	q = 3.9e-4
Nucleosides, nucleotides, and analogues	3	60.0	0.05×	q < 0.0001
Organic salts	1	0.2	4.43×	not tested
Organosulfur compounds	6	4.5	1.34×	not tested
Phenylpropanoids and polyketides	5	4.5	1.11×	not tested
Mixed metal/non-metal compounds	1	4.6	0.22×	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
DB08375	CEF	(2R)-2-[(1R)-1-[[(2Z)-2-(2-Amino-1,3-thiazol-4-yl)-2-methoxyiminoacetyl]amino]-2-oxoethyl]-5-methylidene-2H-1,3-thiazine-4-carboxylic acid	44
DB03530	CAZ	Acylated ceftazidime	26
DB03834	TBE	(3S)-3-(dioxidosulfanyl)-N-[(1Z)-3-oxoprop-1-en-1-yl]-4-(1H-1,2,3-triazol-1-yl)-D-valine	22
DB09157	CO2	Carbon dioxide	21
DB04035	CB4	Ceftazidime BATSI	19
DB00142	GLU	Glutamic acid	18
DB02145	1BO	Butyl alcohol	13
DB04133	CED	Degraded Cephaloridine	13
DB00145	GLY	Glycine	12
DB00355	AZR	Aztreonam	12
DB08551	SM2	3-{(R)-(Dihydroxyboryl)[(2-thienylacetyl)amino]methyl}benzoic acid	12
DB12107	4D6	Vaborbactam	11
DB00513	ACA	Aminocaproic acid	10
DB03658	AXL	(2R,4S)-2-[(1R)-1-{[(2R)-2-Amino-2-(4-hydroxyphenyl)acetyl]amino}-2-oxoethyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid	10
DB04360	BZB	Benzo[B]Thiophene-2-Boronic Acid	10
DB00130	GLN	L-Glutamine	9
DB09324	0RN	Sulbactam	9
DB15232	63J	Telaglenastat	8
DB00766	J01	Clavulanic acid	7
DB01896	APB	M-Aminophenylboronic Acid	7

Most frequently bound compounds

PDB ligand	Name	Domains in contact
CL	CHLORIDE ION	214
NXL	(2S,5R)-1-formyl-5-[(sulfooxy)amino]piperidine-2-carboxamide	123
NAmetal	SODIUM ION	71
IM2	(5R)-5-[(1S,2R)-1-formyl-2-hydroxypropyl]-3-[(2-{[(E)-iminomethyl]amino}ethyl)sulfanyl]-4,5-dihydro-1H-pyrrole-2-carboxylic acid	45
ZNmetal	ZINC ION	41
CDmetal	CADMIUM ION	40
PNM	OPEN FORM - PENICILLIN G	39
MER	(4R,5S)-3-{[(3S,5S)-5-(dimethylcarbamoyl)pyrrolidin-3-yl]sulfanyl}-5-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-4-methyl-4,5-dihydro-1H-pyrrole-2-carboxylic acid	36
9F2	Ceftriaxone	34
TSL	TRANS-ENAMINE INTERMEDIATE OF SULBACTAM	34
CEF	CEFOTAXIME, C3' cleaved, open, bound form	33
CAmetal	CALCIUM ION	28
CAZ	ACYLATED CEFTAZIDIME	27
ID1	Imipenem	27
IOD	IODIDE ION	27
Y33	(5R)-3-{[(3S,5S)-5-(dimethylcarbamoyl)pyrrolidin-3-yl]sulfanyl}-5-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-5-methyl-4,5-dihydro-1H-pyrrole-2-carboxylic acid	27
Kmetal	POTASSIUM ION	25
CO2	CARBON DIOXIDE	24
BAmetal	BARIUM ION	23
TBE	TAZOBACTAM INTERMEDIATE	22