X-group (possible homology)

2499 Subtilisin-like

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Ligands and drugs

2,864

Member domains

615

with ligand contacts (≤ 4 Å)

21.5% of members

606

with DrugDomain annotations

21.2% of members

358

with a DrugBank compound

12.5% 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)

8.3

Superclasses per 20 proteins

broader than 63% 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	51	27.1	1.88×	q < 0.0001
Homogeneous non-metal compounds	17	11.9	1.43×	q = 0.15
Organic acids and derivatives	9	8.5	1.05×	q = 0.90
Organic oxygen compounds	9	11.0	0.82×	q = 0.69
Organoheterocyclic compounds	3	8.5	0.35×	q = 0.06
Lipids and lipid-like molecules	1	6.2	0.16×	q = 0.03
Nucleosides, nucleotides, and analogues	0	15.3	0	q < 0.0001
Organohalogen compounds	1	0.2	6.36×	not tested
Benzenoids	10	4.0	2.48×	not tested
Phenylpropanoids and polyketides	2	1.2	1.74×	not tested
Organic nitrogen compounds	2	1.8	1.14×	not tested
Organosulfur compounds	1	1.1	0.88×	not tested
Mixed metal/non-metal compounds	1	1.2	0.86×	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
DB00141	NAG	N-Acetylglucosamine	30
DB03297	PMS	Benzylsulfonic acid	13
DB03266	PTD	Glutaral	4
DB04491	DFP	Diisopropylphosphono Group	4
DB01694	TAR	D-tartaric acid	3
DB02175	MLA	Malonic acid	3
DB11932	EI3	Abametapir	3
DB03309	NHE	N-cyclohexyltaurine	2
DB11068	SE4	Selenic acid	2
DB18313	TCA	Cinnamic acid	2
DB00117	HIS	Histidine	1
DB00302	AMH	Tranexamic acid	1
DB00356	CLW	Chlorzoxazone	1
DB01811	3ID	3h-Indole-5,6-Diol	1
DB01833	GGB	Canavanine	1
DB02579	AKR	Acrylic Acid	1
DB02701	NCA	Nicotinamide	1
DB02721	PYZ	4-Iodopyrazole	1
DB02810	MHA	N-(2-Acetamido)Iminodiacetic Acid	1
DB03709	BCN	Bicine	1

Most frequently bound compounds

PDB ligand	Name	Domains in contact
CAmetal	CALCIUM ION	434
NAmetal	SODIUM ION	143
CL	CHLORIDE ION	62
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	30
PMS	phenylmethanesulfonic acid	12
ZNmetal	ZINC ION	12
15P	POLYETHYLENE GLYCOL (N=34)	11
Kmetal	POTASSIUM ION	7
CCN	ACETONITRILE	6
HGmetal	MERCURY (II) ION	5
DFP	DIISOPROPYL PHOSPHONATE	4
PTD	PENTANEDIAL	4
EI3	5-methyl-2-(5-methylpyridin-2-yl)pyridine	3
I3C	5-amino-2,4,6-triiodobenzene-1,3-dicarboxylic acid	3
IOD	IODIDE ION	3
MGmetal	MAGNESIUM ION	3
PRmetal	PRASEODYMIUM ION	3
47E	(2R)-(3-chlorophenyl)(hydroxy)ethanoic acid	2
89N	(2E)-but-2-ene-1,4-diol	2
AZI	AZIDE ION	2