X-group (possible homology)

2498 Zincin-like

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Ligands and drugs

14,139

Member domains

4,606

with ligand contacts (≤ 4 Å)

32.6% of members

3,808

with DrugDomain annotations

26.9% of members

2,854

with a DrugBank compound

20.2% 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.

288

Proteins with classified ligands

Superclasses bound (of 23)

9.5

Superclasses per 20 proteins

broader than 89% 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
Mixed metal/non-metal compounds	26	6.0	4.36×	q < 0.0001
Homogeneous metal compounds	275	139.4	1.97×	q < 0.0001
Organic acids and derivatives	78	43.9	1.77×	q < 0.0001
Phenylpropanoids and polyketides	10	5.9	1.69×	q = 0.14
Organic nitrogen compounds	14	9.1	1.55×	q = 0.17
Benzenoids	30	20.8	1.45×	q = 0.06
Organic oxygen compounds	57	56.6	1.01×	q = 0.98
Homogeneous non-metal compounds	53	61.1	0.87×	q = 0.35
Organoheterocyclic compounds	27	43.7	0.62×	q = 1.0e-2
Organosulfur compounds	3	5.8	0.51×	q = 0.37
Nucleosides, nucleotides, and analogues	33	78.5	0.42×	q < 0.0001
Lipids and lipid-like molecules	8	31.6	0.25×	q < 0.0001
Organometallic compounds	1	0.4	2.47×	not tested
Organohalogen compounds	1	0.8	1.24×	not tested
Hydrocarbons	1	2.0	0.50×	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
DB16833	ADP	Adenosine disphosphate	860
DB00141	NAG	N-Acetylglucosamine	514
DB00171	ATP	ATP	341
DB00123	LYS	Lysine	66
DB00161	VAL	Valine	54
DB04349	PGO	(S)-propane-1,2-diol	32
DB00786	—	Marimastat	28
DB00551	HAE	Acetohydroxamic acid	27
DB11326	BO3	Boric acid	21
DB03424	BES	Ubenimex	20
DB02930	AGS	Adenosine 5'-[gamma-thio]triphosphate	18
DB03709	BCN	Bicine	17
DB00125	ARG	Arginine	14
DB00128	ASP	Aspartic acid	14
DB02557	RDF	Phosphoramidon	14
DB03880	BAT	Batimastat	13
DB00149	LEU	Leucine	12
DB08271	NGH	N-ISOBUTYL-N-[4-METHOXYPHENYLSULFONYL]GLYCYL HYDROXAMIC ACID	12
DB00133	SER	Serine	11
DB00172	PRO	Proline	11

Most frequently bound compounds

PDB ligand	Name	Domains in contact
ZNmetal	ZINC ION	2,401
ADP	ADENOSINE-5'-DIPHOSPHATE	993
CAmetal	CALCIUM ION	985
MGmetal	MAGNESIUM ION	952
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	693
AF3	ALUMINUM FLUORIDE	520
ATP	ADENOSINE-5'-TRIPHOSPHATE	515
CL	CHLORIDE ION	335
BEF	BERYLLIUM TRIFLUORIDE ION	191
NAmetal	SODIUM ION	120
Kmetal	POTASSIUM ION	70
LYS	LYSINE	69
VAL	VALINE	55
ANP	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER	48
PGO	S-1,2-PROPANEDIOL	37
P6G	HEXAETHYLENE GLYCOL	35
NImetal	NICKEL (II) ION	34
CDmetal	CADMIUM ION	30
HAE	ACETOHYDROXAMIC ACID	27
BO3	BORIC ACID	26