X-group (possible homology)

873 H-NOX domain

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Ligands and drugs

968

Member domains

197

with ligand contacts (≤ 4 Å)

20.4% of members

199

with DrugDomain annotations

20.6% of members

178

with a DrugBank compound

18.4% 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)

8.9

Superclasses per 20 proteins

broader than 76% 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	7	10.2	0.69×	q = 0.26
Nucleosides, nucleotides, and analogues	0	5.7	0	q = 4.9e-3
Phenylpropanoids and polyketides	2	0.4	4.64×	not tested
Lipids and lipid-like molecules	9	2.3	3.90×	not tested
Benzenoids	4	1.5	2.64×	not tested
Organosulfur compounds	1	0.4	2.35×	not tested
Organic nitrogen compounds	1	0.7	1.51×	not tested
Homogeneous non-metal compounds	6	4.5	1.35×	not tested
Organoheterocyclic compounds	3	3.2	0.94×	not tested
Organic acids and derivatives	1	3.2	0.31×	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	94
DB03796	PLM	Palmitic Acid	40
DB09140	OXY	Oxygen	20
DB02175	MLA	Malonic acid	10
DB11588	CMO	Carbon monoxide	10
DB03255	IPH	Phenol	9
DB16126	Z90	Cinaciguat	5
DB08231	MYR	Myristic acid	3
DB08342	—	—	3
DB08931	GZO	Riociguat	3
DB01688	PCR	P-Cresol	2
DB01957	3CH	3-Chlorophenol	2
DB02232	CAQ	1,2-Dihydroxybenzene	2
DB02671	1MZ	1-Methylimidazole	2
DB04052	2MP	3,4-Xylenol	2
DB04417	NPO	P-Nitrophenol	2
DB16700	XZ7	Runcaciguat	2
DB00435	—	—	1
DB01020	—	—	1
DB09241	—	—	1

Most frequently bound compounds

PDB ligand	Name	Domains in contact
HEM	PROTOPORPHYRIN IX CONTAINING FE	98
ZNmetal	ZINC ION	44
PLM	PALMITIC ACID	37
OXY	OXYGEN MOLECULE	20
CL	CHLORIDE ION	14
CMO	CARBON MONOXIDE	10
IPH	PHENOL	9
MLA	MALONIC ACID	9
NO	NITRIC OXIDE	8
XE	XENON	8
NAmetal	SODIUM ION	7
MNH	MANGANESE PROTOPORPHYRIN IX	6
Z90	4-({(4-carboxybutyl)[2-(2-{[4-(2-phenylethyl)benzyl]oxy}phenyl)ethyl]amino}methyl)benzoic acid	5
1DX	4-({(4-carboxybutyl)[2-(5-fluoro-2-{[4'-(trifluoromethyl)biphenyl-4-yl]methoxy}phenyl)ethyl]amino}methyl)benzoic acid	4
MYR	MYRISTIC ACID	3
1MF	4-{[(4-carboxybutyl)(2-{2-[(4'-phenoxybiphenyl-4-yl)methoxy]phenyl}ethyl)amino]methyl}benzoic acid	2
1MZ	1-METHYLIMIDAZOLE	2
2MP	3,4-DIMETHYLPHENOL	2
3CH	3-CHLOROPHENOL	2
5JC	2,4-dichlorophenol	2