X-group (possible homology)

1128 LYR protein

Open in classification tree →

Ligands and drugs

1,058

Member domains

540

with ligand contacts (≤ 4 Å)

51.0% of members

345

with DrugDomain annotations

32.6% of members

with a DrugBank compound

7.2% 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.

Proteins with classified ligands

Superclasses bound (of 23)

2.0

Superclasses per 20 proteins

narrower than 99% 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 metal compounds	0	12.6	0	q < 0.0001
Homogeneous non-metal compounds	0	5.5	0	q = 6.7e-3
Nucleosides, nucleotides, and analogues	0	7.1	0	q = 1.4e-3
Organic oxygen compounds	0	5.1	0	q = 0.01
Organic acids and derivatives	25	4.0	6.30×	not tested
Lipids and lipid-like molecules	6	2.9	2.10×	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
DB03429	CDL	Tetrastearoyl cardiolipin	53
DB03912	PNS	D-pantetheine 4'-phosphate	14
DB00974	EDT	Edetic acid	5
DB02777	PLC	Diundecyl Phosphatidyl Choline	4

Most frequently bound compounds

PDB ligand	Name	Domains in contact
EHZ	~{S}-[2-[3-[[(2~{R})-3,3-dimethyl-2-oxidanyl-4-phosphonooxy-butanoyl]amino]propanoylamino]ethyl] (3~{S})-3-oxidanyltetradecanethioate	191
8Q1	S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate	185
ZMP	S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] tetradecanethioate	142
PLC	DIUNDECYL PHOSPHATIDYL CHOLINE	20
3PE	1,2-Distearoyl-sn-glycerophosphoethanolamine	17
PNS	4'-PHOSPHOPANTETHEINE	16
CDL	CARDIOLIPIN	7
EDT	{[-(BIS-CARBOXYMETHYL-AMINO)-ETHYL]-CARBOXYMETHYL-AMINO}-ACETIC ACID	6
PM8	S-(2-{[N-(2-HYDROXY-4-{[HYDROXY(OXIDO)PHOSPHINO]OXY}-3,3-DIMETHYLBUTANOYL)-BETA-ALANYL]AMINO}ETHYL) DECANETHIOATE	6
PC7	(7S)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSAN-1-AMINIUM 4-OXIDE	2