X-group (possible homology)

4048 Second alpha-helical domain in heme-dependent catalases

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Ligands and drugs

768

Member domains

238

with ligand contacts (≤ 4 Å)

31.0% of members

204

with DrugDomain annotations

26.6% of members

157

with a DrugBank compound

20.4% 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)

7.0

Superclasses per 20 proteins

narrower than 59% 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	10	5.5	1.83×	q = 0.06
Homogeneous metal compounds	5	9.7	0.52×	q = 0.07
Homogeneous non-metal compounds	3	4.2	0.71×	not tested
Benzenoids	1	1.4	0.69×	not tested
Organoheterocyclic compounds	2	3.0	0.66×	not tested
Organic acids and derivatives	2	3.1	0.66×	not tested
Organic oxygen compounds	2	3.9	0.51×	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
DB02338	NDP	NADPH	84
DB00141	NAG	N-Acetylglucosamine	4
DB02232	CAQ	1,2-Dihydroxybenzene	4
DB03110	2CH	2-Chlorophenol	4
DB09526	HQE	Hydroquinone	4
DB11085	RCO	Resorcinol	4
DB11091	PEO	Hydrogen peroxide	4
DB11359	JZ3	Guaiacol	4
DB00160	ALA	Alanine	2
DB01213	—	Fomepizole	1
DB01694	TAR	D-tartaric acid	1
DB03461	NAP	Nicotinamide adenine dinucleotide phosphate	1
DB09061	—	Cannabidiol	1
DB09096	—	—	1
DB14011	—	—	1
DB14556	F50	Peracetic acid	1

Most frequently bound compounds

PDB ligand	Name	Domains in contact
NDP	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE	110
CAmetal	CALCIUM ION	35
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	9
3TR	3-AMINO-1,2,4-TRIAZOLE	8
LLR	(~{S})-azanyl-[2-[[3-bromanyl-4-(diethylamino)phenyl]methyl]hydrazinyl]methanethiol	4
PEO	HYDROGEN PEROXIDE	4
CAQ	CATECHOL	3
CL	CHLORIDE ION	3
HQE	benzene-1,4-diol	3
2CH	2-CHLOROPHENOL	2
F50	ETHANEPEROXOIC ACID	2
JZ3	Guaiacol	2
AE3	2-(2-ETHOXYETHOXY)ETHANOL	1
NAP	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE	1
TAR	D(-)-TARTARIC ACID	1