X-group (possible homology)

7523 Periplasmic binding protein-like II

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Ligands and drugs

19,672

Member domains

7,209

with ligand contacts (≤ 4 Å)

36.6% of members

6,942

with DrugDomain annotations

35.3% of members

4,962

with a DrugBank compound

25.2% 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.

474

Proteins with classified ligands

Superclasses bound (of 23)

8.6

Superclasses per 20 proteins

broader than 69% 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	205	72.3	2.83×	q < 0.0001
Organic nitrogen compounds	29	14.9	1.95×	q = 1.9e-3
Mixed metal/non-metal compounds	17	9.8	1.73×	q = 0.05
Homogeneous non-metal compounds	153	100.6	1.52×	q < 0.0001
Organic oxygen compounds	100	93.1	1.07×	q = 0.49
Organosulfur compounds	9	9.6	0.94×	q = 1.00
Phenylpropanoids and polyketides	9	9.7	0.93×	q = 1.00
Benzenoids	31	34.2	0.91×	q = 0.73
Homogeneous metal compounds	170	229.4	0.74×	q < 0.0001
Organoheterocyclic compounds	46	71.9	0.64×	q = 1.6e-3
Lipids and lipid-like molecules	20	52.0	0.38×	q < 0.0001
Nucleosides, nucleotides, and analogues	11	129.2	0.09×	q < 0.0001
Organometallic compounds	2	0.7	3.00×	not tested
Miscellaneous inorganic compounds	1	0.4	2.87×	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
DB00142	GLU	Glutamic acid	843
DB00141	NAG	N-Acetylglucosamine	336
DB12393	ZK1	Fanapanel	241
DB00145	GLY	Glycine	216
DB00125	ARG	Arginine	97
DB00134	MET	Methionine	80
DB00606	CYZ	Cyclothiazide	78
DB02999	QUS	Quisqualic acid	76
DB03566	SPD	Spermidine	75
DB00117	HIS	Histidine	55
DB00171	ATP	ATP	52
DB00130	GLN	L-Glutamine	50
DB01632	PRP	5-O-phosphono-alpha-D-ribofuranosyl diphosphate	45
DB09157	CO2	Carbon dioxide	45
DB04517	DPM	Dipyrromethane Cofactor	42
DB02057	AMQ	(S)-AMPA	40
DB02966	FWD	Fluoro-Willardiine	36
DB00131	AMP	Adenosine phosphate	30
DB04265	SLB	N-acetyl-beta-neuraminic acid	30
DB00151	CYS	Cysteine	28

Most frequently bound compounds

PDB ligand	Name	Domains in contact
GLU	GLUTAMIC ACID	787
CL	CHLORIDE ION	774
ZNmetal	ZINC ION	719
FEmetal	FE (III) ION	489
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	303
CAmetal	CALCIUM ION	260
ZK1	{[7-morpholin-4-yl-2,3-dioxo-6-(trifluoromethyl)-3,4-dihydroquinoxalin-1(2H)-yl]methyl}phosphonic acid	239
NAmetal	SODIUM ION	188
KAI	3-(CARBOXYMETHYL)-4-ISOPROPENYLPROLINE	182
GLY	GLYCINE	178
MGmetal	MAGNESIUM ION	165
ARG	ARGININE	105
MET	METHIONINE	82
CYZ	CYCLOTHIAZIDE	78
FWF	N,N'-[biphenyl-4,4'-diyldi(2R)propane-2,1-diyl]dipropane-2-sulfonamide	76
SPD	SPERMIDINE	75
QUS	(S)-2-AMINO-3-(3,5-DIOXO-[1,2,4]OXADIAZOLIDIN-2-YL)-PROPIONIC ACID	72
FGO	[(1S,3R,3aR,6aS)-3-(2-azanyl-6-oxidanylidene-1H-purin-9-yl)-5,5-bis(oxidanyl)-1,3,3a,4,6,6a-hexahydrocyclopenta[c]furan-1-yl]methyl [(2R,3S,4R,5R)-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-2-(hydroxymethyl)-4-oxidanyl-oxolan-3-yl] hydrogen phosphate	68
GLN	GLUTAMINE	56
HIS	HISTIDINE	56