X-group (possible homology)

3702 Penicillin binding protein dimerisation domain

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Ligands and drugs

349

Member domains

123

with ligand contacts (≤ 4 Å)

35.2% of members

with DrugDomain annotations

20.6% of members

with a DrugBank compound

6.9% 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)

—

Superclasses per 20 proteins

fewer than 20 proteins: too few to compare at equal depth

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
Homogeneous metal compounds	10	7.3	1.38×	q = 0.26
Homogeneous non-metal compounds	9	3.2	2.83×	not tested
Organic nitrogen compounds	1	0.5	2.12×	not tested
Organic oxygen compounds	4	3.0	1.36×	not tested
Organoheterocyclic compounds	2	2.3	0.88×	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
DB08357	P4G	Diethylene glycol diethyl ether	1

Most frequently bound compounds

PDB ligand	Name	Domains in contact
CDmetal	CADMIUM ION	36
CL	CHLORIDE ION	30
MUR	beta-muramic acid	15
COmetal	COBALT (II) ION	6
1W8	Ceftaroline	4
ZNmetal	ZINC ION	4
AMV	methyl 2-acetamido-3-O-[(1R)-1-carboxyethyl]-2-deoxy-beta-D-glucopyranoside	2
BR	BROMIDE ION	2
CAZ	ACYLATED CEFTAZIDIME	2
QLN	3-[2-[(~{E})-2-(4-ethynylphenyl)ethenyl]-4-oxidanylidene-quinazolin-3-yl]benzoic acid	2
QNZ	(E)-3-(2-(4-cyanostyryl)-4-oxoquinazolin-3(4H)-yl)benzoic acid	2
12P	DODECAETHYLENE GLYCOL	1
CEF	CEFOTAXIME, C3' cleaved, open, bound form	1
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	1
P4G	1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE	1
TMO	trimethylamine oxide	1