X-group (possible homology)

172 Citrate synthase-like

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Ligands and drugs

992

Member domains

354

with ligand contacts (≤ 4 Å)

35.7% of members

316

with DrugDomain annotations

31.9% of members

262

with a DrugBank compound

26.4% 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)

6.4

Superclasses per 20 proteins

narrower than 70% 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
Nucleosides, nucleotides, and analogues	14	7.9	1.77×	q = 0.03
Homogeneous non-metal compounds	9	6.2	1.46×	q = 0.33
Homogeneous metal compounds	4	14.0	0.28×	q = 3.8e-4
Organic oxygen compounds	1	5.7	0.18×	q = 0.05
Organic acids and derivatives	18	4.4	4.07×	not tested
Lipids and lipid-like molecules	8	3.2	2.51×	not tested
Benzenoids	1	2.1	0.48×	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
DB02637	OAA	Oxaloacetate Ion	74
DB01992	COA	Coenzyme A	73
DB00139	SIN	Succinic acid	9
DB00119	PYR	Pyruvic acid	6
DB00157	NAI	NADH	4
DB02579	AKR	Acrylic Acid	4
DB01969	COF	Trifluoroacetonyl coenzyme A	3
DB03182	FCX	alpha-Fluoro-carboxymethyldethia coenzyme A complex	2
DB04230	NMX	Nitromethyldethia coenzyme A	2
DB14128	NAD	Nadide	2
DB14756	SRT	meso-Tartaric acid	2
DB00151	CYS	Cysteine	1
DB01846	CAO	Oxidized coenzyme A	1
DB03499	—	D-Malic acid	1
DB04272	—	Citric acid	1
DB11936	—	—	1

Most frequently bound compounds

PDB ligand	Name	Domains in contact
OAA	OXALOACETATE ION	95
COA	COENZYME A	84
ACO	ACETYL COENZYME *A	47
Q5B	(3S)-citryl-Coenzyme A	24
CL	CHLORIDE ION	20
LMR	(2S)-2-hydroxybutanedioic acid	10
CMC	CARBOXYMETHYL COENZYME *A	9
SIN	SUCCINIC ACID	9
UNL	Unknown ligand	9
9JT	N-phenyl-2-selanylbenzamide	8
MGmetal	MAGNESIUM ION	8
CMX	CARBOXYMETHYLDETHIA COENZYME *A	7
NAmetal	SODIUM ION	6
PYR	PYRUVIC ACID	6
AKR	ACRYLIC ACID	4
COZ	COENZYME A	4
IOD	IODIDE ION	4
SDX	s-citryldethia Coenzyme A	4
8JD	[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (3R)-4-[(3-{[2-(ethylsulfanyl)ethyl]amino}-3-oxopropyl)amino]-3-hydroxy-2,2-dimethyl-4-oxobutyl dihydrogen diphosphate (non-preferred name)	2
CAmetal	CALCIUM ION	2