X-group (possible homology)

327 Alpha-lytic protease prodomain-like

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Ligands and drugs

29,218

Member domains

1,919

with ligand contacts (≤ 4 Å)

6.6% of members

1,575

with DrugDomain annotations

5.4% of members

1,073

with a DrugBank compound

3.7% 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.

169

Proteins with classified ligands

Superclasses bound (of 23)

7.9

Superclasses per 20 proteins

broader than 54% 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	105	46.1	2.28×	q < 0.0001
Homogeneous non-metal compounds	39	35.9	1.09×	q = 0.65
Homogeneous metal compounds	85	81.8	1.04×	q = 0.72
Organic nitrogen compounds	5	5.3	0.94×	q = 1.00
Organic acids and derivatives	24	25.8	0.93×	q = 0.88
Benzenoids	11	12.2	0.90×	q = 0.92
Organoheterocyclic compounds	9	25.6	0.35×	q = 2.9e-4
Lipids and lipid-like molecules	6	18.6	0.32×	q = 1.9e-3
Organic oxygen compounds	10	33.2	0.30×	q < 0.0001
Alkaloids and derivatives	1	0.6	1.76×	not tested
Organosulfur compounds	3	3.4	0.88×	not tested
Phenylpropanoids and polyketides	2	3.5	0.58×	not tested
Mixed metal/non-metal compounds	1	3.5	0.29×	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
DB00118	SAM	Ademetionine	220
DB00131	AMP	Adenosine phosphate	122
DB03075	PPK	(Diphosphono)Aminophosphonic Acid	118
DB00171	ATP	ATP	56
DB00640	ADN	Adenosine	45
DB03345	BME	Mercaptoethanol	42
DB03896	3PO	Triphosphoric acid	35
DB00134	MET	Methionine	31
DB01992	COA	Coenzyme A	29
DB03434	MPO	3-(N-morpholino)propanesulfonic acid	25
DB02596	APC	alpha,beta-Methyleneadenosine 5'-triphosphate	19
DB03230	PRX	Adenosine-5'-Propylphosphate	19
DB02282	MTA	5'-S-methyl-5'-thioadenosine	18
DB16833	ADP	Adenosine disphosphate	17
DB02309	XMP	5-monophosphate-9-beta-D-ribofuranosyl xanthine	12
DB03912	PNS	D-pantetheine 4'-phosphate	12
DB03909	ACP	Adenosine-5'-[Beta, Gamma-Methylene]Triphosphate	10
DB03247	FMN	Flavin mononucleotide	9
DB03611	AMB	L-2-amino-4-methoxy-cis-but-3-enoic acid	8
DB14078	MDN	Medronic acid	8

Most frequently bound compounds

PDB ligand	Name	Domains in contact
MGmetal	MAGNESIUM ION	488
SAM	S-ADENOSYLMETHIONINE	288
Kmetal	POTASSIUM ION	190
AMP	ADENOSINE MONOPHOSPHATE	142
CL	CHLORIDE ION	124
PPK	(DIPHOSPHONO)AMINOPHOSPHONIC ACID	117
ZNmetal	ZINC ION	68
POP	PYROPHOSPHATE 2-	62
ATP	ADENOSINE-5'-TRIPHOSPHATE	60
NAmetal	SODIUM ION	53
ADN	ADENOSINE	46
BME	BETA-MERCAPTOETHANOL	41
4LU	1-deoxy-5-O-phosphono-1-(3,3,4,5-tetramethyl-9,11-dioxo-2,3,8,9,10,11-hexahydro-7H-quinolino[1,8-fg]pteridin-12-ium-7-yl)-D-ribitol	40
CAmetal	CALCIUM ION	40
COA	COENZYME A	39
BYN	hydroxylated prenyl-FMN	37
ANP	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER	35
3PO	TRIPHOSPHATE	34
MET	METHIONINE	27
MPO	3[N-MORPHOLINO]PROPANE SULFONIC ACID	25