X-group (possible homology)

4028 Barrel domain in heme-dependent catalases

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Ligands and drugs

787

Member domains

595

with ligand contacts (≤ 4 Å)

75.6% of members

543

with DrugDomain annotations

69.0% of members

420

with a DrugBank compound

53.4% 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 58% 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 non-metal compounds	17	6.2	2.76×	q < 0.0001
Nucleosides, nucleotides, and analogues	10	7.9	1.26×	q = 0.48
Homogeneous metal compounds	12	14.0	0.85×	q = 0.54
Organic oxygen compounds	3	5.7	0.53×	q = 0.32
Organoheterocyclic compounds	10	4.4	2.27×	not tested
Benzenoids	1	2.1	0.48×	not tested
Lipids and lipid-like molecules	1	3.2	0.31×	not tested
Organic acids and derivatives	1	4.4	0.23×	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
DB18267	HEM	Ferroheme	394
DB02338	NDP	NADPH	84
DB00141	NAG	N-Acetylglucosamine	9
DB09526	HQE	Hydroquinone	4
DB11085	RCO	Resorcinol	4
DB11091	PEO	Hydrogen peroxide	4
DB02210	HEZ	Hexane-1,6-Diol	2
DB03110	2CH	2-Chlorophenol	2
DB11359	JZ3	Guaiacol	2
DB14556	F50	Peracetic acid	2
DB01213	—	Fomepizole	1
DB01694	TAR	D-tartaric acid	1
DB02232	CAQ	1,2-Dihydroxybenzene	1
DB03461	NAP	Nicotinamide adenine dinucleotide phosphate	1
DB09061	—	Cannabidiol	1
DB09096	—	—	1
DB09140	OXY	Oxygen	1
DB14011	—	—	1

Most frequently bound compounds

PDB ligand	Name	Domains in contact
HEM	PROTOPORPHYRIN IX CONTAINING FE	447
HDD	CIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE	166
NDP	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE	112
CL	CHLORIDE ION	67
CAmetal	CALCIUM ION	57
HDE	CIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE 17R, 18S	40
H2S	HYDROSULFURIC ACID	32
NAmetal	SODIUM ION	19
O	OXYGEN ATOM	14
NO	NITRIC OXIDE	12
3TR	3-AMINO-1,2,4-TRIAZOLE	11
AZI	AZIDE ION	9
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	9
Kmetal	POTASSIUM ION	8
CYN	CYANIDE ION	6
PEO	HYDROGEN PEROXIDE	5
2CH	2-CHLOROPHENOL	4
CAQ	CATECHOL	4
HQE	benzene-1,4-diol	4
JZ3	Guaiacol	4