X-group (possible homology)

3921 Na(+)-translocating NADH-quinone reductase subunit D

Open in classification tree →

Ligands and drugs

462

Member domains

with ligand contacts (≤ 4 Å)

16.9% of members

with DrugDomain annotations

7.8% of members

with a DrugBank compound

2.8% 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
Lipids and lipid-like molecules	5	0.9	5.69×	not tested
Nucleosides, nucleotides, and analogues	4	2.2	1.83×	not tested
Organic acids and derivatives	2	1.2	1.64×	not tested
Homogeneous metal compounds	3	3.9	0.78×	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
DB03247	FMN	Flavin mononucleotide	12
DB00123	LYS	Lysine	2
DB04327	PEE	Phosphatidylethanolamine	1

Most frequently bound compounds

PDB ligand	Name	Domains in contact
FES	FE2/S2 (INORGANIC) CLUSTER	76
3PE	1,2-Distearoyl-sn-glycerophosphoethanolamine	12
FMN	FLAVIN MONONUCLEOTIDE	10
NAmetal	SODIUM ION	6
PTY	PHOSPHATIDYLETHANOLAMINE	6
CAmetal	CALCIUM ION	2
FEmetal	FE (III) ION	2
LYS	LYSINE	2
PEE	1,2-dioleoyl-sn-glycero-3-phosphoethanolamine	2