X-group (possible homology)

7 PDZ domain

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Ligands and drugs

5,383

Member domains

777

with ligand contacts (≤ 4 Å)

14.4% of members

744

with DrugDomain annotations

13.8% of members

479

with a DrugBank compound

8.9% 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)

8.1

Superclasses per 20 proteins

broader than 60% 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
Homogeneous non-metal compounds	34	13.6	2.50×	q < 0.0001
Organic acids and derivatives	8	9.8	0.82×	q = 0.79
Organoheterocyclic compounds	6	9.7	0.62×	q = 0.29
Homogeneous metal compounds	19	31.0	0.61×	q = 5.7e-3
Organic oxygen compounds	5	12.6	0.40×	q = 0.03
Lipids and lipid-like molecules	1	7.0	0.14×	q = 0.02
Nucleosides, nucleotides, and analogues	0	17.4	0	q < 0.0001
Organohalogen compounds	1	0.2	5.56×	not tested
Organosulfur compounds	4	1.3	3.08×	not tested
Hydrocarbons	1	0.4	2.27×	not tested
Benzenoids	9	4.6	1.95×	not tested
Organic nitrogen compounds	3	2.0	1.49×	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
DB00145	GLY	Glycine	106
DB02517	DGL	D-Glutamic Acid	105
DB00160	ALA	Alanine	31
DB04447	DTT	1,4-Dithiothreitol	7
DB00149	LEU	Leucine	6
DB00125	ARG	Arginine	4
DB00156	THR	Threonine	4
DB02184	DTV	D-1,4-dithiothreitol	4
DB03793	BEZ	Benzoic acid	4
DB07376	ANS	5-(DIMETHYLAMINO)-1-NAPHTHALENESULFONIC ACID(DANSYL ACID)	4
DB01972	—	Guanosine-5'-Monophosphate	3
DB00142	GLU	Glutamic acid	2
DB00143	GSH	Glutathione	2
DB03317	HEC	Ferroheme C	2
DB07114	4MB	4-[(METHYLSULFONYL)AMINO]BENZOIC ACID	2
DB00117	HIS	Histidine	1
DB00122	CHT	Choline	1
DB00161	VAL	Valine	1
DB00812	P1Z	Phenylbutazone	1
DB02219	CXS	3-(cyclohexylamino)propanesulfonic acid	1

Most frequently bound compounds

PDB ligand	Name	Domains in contact
GLY	GLYCINE	108
DGL	D-GLUTAMIC ACID	105
CL	CHLORIDE ION	58
ALA	ALANINE	31
IOD	IODIDE ION	21
NAmetal	SODIUM ION	19
SCN	THIOCYANATE ION	12
ZNmetal	ZINC ION	11
LEU	LEUCINE	6
LV4	1-[2-(trifluoromethyloxy)phenyl]thiourea	6
NImetal	NICKEL (II) ION	6
12P	DODECAETHYLENE GLYCOL	5
LKV	(2~{S})-2-[[(2~{S})-3-methyl-2-(3-oxidanylidene-1~{H}-isoindol-2-yl)butanoyl]amino]propanoic acid	5
SZB	succinimide	5
ACE	ACETYL GROUP	4
ANS	5-(DIMETHYLAMINO)-1-NAPHTHALENESULFONIC ACID(DANSYL ACID)	4
ARG	ARGININE	4
BEZ	BENZOIC ACID	4
BR	BROMIDE ION	4
CAmetal	CALCIUM ION	4