X-group (possible homology)

620 YfiT-like putative metal-dependent hydrolases

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Ligands and drugs

232

Member domains

with ligand contacts (≤ 4 Å)

40.5% of members

with DrugDomain annotations

28.9% of members

with a DrugBank compound

15.5% 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)

4.8

Superclasses per 20 proteins

narrower than 85% 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	11	5.1	2.16×	q = 0.02
Homogeneous metal compounds	16	11.6	1.38×	q = 0.15
Nucleosides, nucleotides, and analogues	0	6.5	0	q = 2.0e-3
Organic nitrogen compounds	1	0.8	1.32×	not tested
Organic acids and derivatives	3	3.7	0.82×	not tested
Organic oxygen compounds	3	4.7	0.64×	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
DB03408	3GC	gamma-Glutamylcysteine	2
DB00133	SER	Serine	1
DB00142	GLU	Glutamic acid	1
DB00156	THR	Threonine	1
DB00160	ALA	Alanine	1
DB01694	TAR	D-tartaric acid	1
DB03309	NHE	N-cyclohexyltaurine	1

Most frequently bound compounds

PDB ligand	Name	Domains in contact
FEmetal	FE (III) ION	38
NImetal	NICKEL (II) ION	21
CL	CHLORIDE ION	17
AVJ	N,N,N-trimethyl-histidine	16
CYS	CYSTEINE	6
HIS	HISTIDINE	6
ZNmetal	ZINC ION	5
COmetal	COBALT (II) ION	4
MGmetal	MAGNESIUM ION	4
MNmetal	MANGANESE (II) ION	4
UCQ	(2~{S})-2-(dimethylamino)-3-(3-methylimidazol-4-yl)propanoic acid	4
AVI	N,N-dimethyl-L-histidine	3
NAmetal	SODIUM ION	3
3GC	GAMMA-GLUTAMYLCYSTEINE	2
BR	BROMIDE ION	2
Kmetal	POTASSIUM ION	2
MRD	(4R)-2-METHYLPENTANE-2,4-DIOL	2
XGZ	Mycothiol	2
CAmetal	CALCIUM ION	1
GLU	GLUTAMIC ACID	1