X-group (possible homology)

2486 ClpP/crotonase

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Ligands and drugs

7,931

Member domains

2,689

with ligand contacts (≤ 4 Å)

33.9% of members

1,917

with DrugDomain annotations

24.2% of members

1,101

with a DrugBank compound

13.9% 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.

124

Proteins with classified ligands

Superclasses bound (of 23)

9.1

Superclasses per 20 proteins

broader than 82% 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
Lipids and lipid-like molecules	31	13.6	2.28×	q < 0.0001
Benzenoids	12	8.9	1.34×	q = 0.37
Homogeneous non-metal compounds	30	26.3	1.14×	q = 0.52
Organic acids and derivatives	19	18.9	1.00×	q = 1.00
Organoheterocyclic compounds	13	18.8	0.69×	q = 0.23
Homogeneous metal compounds	39	60.0	0.65×	q = 4.3e-4
Organic oxygen compounds	15	24.4	0.62×	q = 0.05
Nucleosides, nucleotides, and analogues	20	33.8	0.59×	q = 9.3e-3
Miscellaneous inorganic compounds	1	0.1	11×	not tested
Organosulfur compounds	3	2.5	1.19×	not tested
Hydrocarbons	1	0.9	1.17×	not tested
Organic nitrogen compounds	4	3.9	1.03×	not tested
Phenylpropanoids and polyketides	1	2.5	0.39×	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
DB07497	BTI	5-(hexahydro-2-oxo-1H-thieno[3,4-D]imidazol-6-yl)pentanal	114
DB01992	COA	Coenzyme A	110
DB03059	CAA	Acetoacetyl-CoA	34
DB04519	OCA	Caprylic acid	28
DB02563	HXC	Hexanoyl-CoA	19
DB04045	MCA	(R)-methylmalonyl-CoA	18
DB09140	OXY	Oxygen	17
DB00149	LEU	Leucine	14
DB02910	CO8	Octanoyl-Coenzyme A	14
DB03309	NHE	N-cyclohexyltaurine	14
DB07571	CMQ	N~2~-[(BENZYLOXY)CARBONYL]-N-[(1S,2S)-2-HYDROXY-1-(4-HYDROXYBENZYL)PROPYL]-L-LEUCINAMIDE	14
DB00121	BTN	Biotin	12
DB02906	CAX	(2s,4s)-Alpha-Campholinic Acid	12
DB04183	DXX	Methylmalonic Acid	12
DB07870	H1L	Haloxyfop-P	11
DB00188	BO2	Bortezomib	7
DB04117	DAK	4-(N,N-Dimethylamino)cinnamoyl-CoA	7
DB04491	DFP	Diisopropylphosphono Group	7
DB00139	SIN	Succinic acid	6
DB00173	ADE	Adenine	6

Most frequently bound compounds

PDB ligand	Name	Domains in contact
BTI	5-(HEXAHYDRO-2-OXO-1H-THIENO[3,4-D]IMIDAZOL-6-YL)PENTANAL	190
BTN	BIOTIN	137
BO2	N-[(1R)-1-(DIHYDROXYBORYL)-3-METHYLBUTYL]-N-(PYRAZIN-2-YLCARBONYL)-L-PHENYLALANINAMIDE	133
CL	CHLORIDE ION	122
COA	COENZYME A	109
MGmetal	MAGNESIUM ION	104
NAmetal	SODIUM ION	80
ACO	ACETYL COENZYME *A	72
VSZ	Cystargolide A (bound)	70
1VU	propionyl Coenzyme A	68
CAmetal	CALCIUM ION	65
Kmetal	POTASSIUM ION	64
TW3	~{S}-[2-[3-[[(2~{R})-4-[[[(2~{S},3~{S},4~{S},5~{S})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethyl] 3-methylbut-2-enethioate	60
YE1	[(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-4-HYDROXY-3-(PHOSPHONOOXY)TETRAHYDROFURAN-2-YL]METHYL (3R)-4-({3-[(2-{[(3,5-DIHYDROXYPHENYL)ACETYL]AMINO}ETHYL)AMINO]-3-OXOPROPYL}AMINO)-3-HYDROXY-2,2-DIMETHYL-4-OXOBUTYL DIHYDROGEN DIPHOSPHATE	42
NImetal	NICKEL (II) ION	35
1HA	1-hydroxy-2-naphthoyl-CoA	33
CAA	ACETOACETYL-COENZYME A	33
ZNmetal	ZINC ION	29
9DF	(6S,9aS)-6-[(2S)-butan-2-yl]-8-(naphthalen-1-ylmethyl)-4,7-bis(oxidanylidene)-N-[4,4,4-tris(fluoranyl)butyl]-3,6,9,9a-tetrahydro-2H-pyrazino[1,2-a]pyrimidine-1-carboxamide	28
AI4	4-[1-[3-[4-[(4-fluoranyl-2-methyl-1H-indol-5-yl)oxy]-6-methoxy-quinazolin-7-yl]oxypropyl]piperidin-4-yl]benzamide	28