X-group (possible homology)

601 Four-helical up-and-down bundle

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Ligands and drugs

12,206

Member domains

1,420

with ligand contacts (≤ 4 Å)

11.6% of members

1,220

with DrugDomain annotations

10.0% of members

916

with a DrugBank compound

7.5% 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.

134

Proteins with classified ligands

Superclasses bound (of 23)

8.5

Superclasses per 20 proteins

broader than 67% 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	43	28.4	1.51×	q = 8.3e-3
Organoheterocyclic compounds	21	20.3	1.03×	q = 0.87
Homogeneous metal compounds	59	64.9	0.91×	q = 0.42
Lipids and lipid-like molecules	11	14.7	0.75×	q = 0.48
Nucleosides, nucleotides, and analogues	25	36.5	0.69×	q = 0.04
Organic oxygen compounds	14	26.3	0.53×	q = 0.01
Benzenoids	5	9.7	0.52×	q = 0.19
Organic acids and derivatives	9	20.4	0.44×	q = 7.8e-3
Miscellaneous inorganic compounds	1	0.1	10×	not tested
Mixed metal/non-metal compounds	6	2.8	2.16×	not tested
Phenylpropanoids and polyketides	3	2.8	1.09×	not tested
Organosulfur compounds	1	2.7	0.37×	not tested
Organic nitrogen compounds	1	4.2	0.24×	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
DB03317	HEC	Ferroheme C	255
DB18267	HEM	Ferroheme	143
DB03147	FAD	Flavin adenine dinucleotide	117
DB08440	PXX	N-1,10-phenanthrolin-5-ylacetamide	28
DB00551	HAE	Acetohydroxamic acid	25
DB18573	17F	1,2-Dioleoyl-sn-glycero-3-phospho-L-serine	19
DB03426	DGD	Digalactosyl Diacyl Glycerol (Dgdg)	16
DB03690	PCW	(Z,Z)-4-Hydroxy-N,N,N-Trimethyl-10-Oxo-7-[(1-Oxo-9-Octadecenyl)Oxy]-3,5,9-Trioxa-4-Phosphaheptacos-18-En-1-Aminium-4-Oxide	16
DB00452	NMY	Framycetin	13
DB00877	RAP	Sirolimus	13
DB00131	AMP	Adenosine phosphate	12
DB11588	CMO	Carbon monoxide	11
DB00128	ASP	Aspartic acid	10
DB00126	ASC	Ascorbic acid	9
DB02596	APC	alpha,beta-Methyleneadenosine 5'-triphosphate	6
DB04160	PPV	Pyrophosphoric acid	6
DB02013	FEA	Iron azide hydrate	5
DB04540	CLR	Cholesterol	5
DB00139	SIN	Succinic acid	4
DB00150	TRP	Tryptophan	4

Most frequently bound compounds

PDB ligand	Name	Domains in contact
HEC	HEME C	233
ZNmetal	ZINC ION	230
HEM	PROTOPORPHYRIN IX CONTAINING FE	158
CL	CHLORIDE ION	128
FAD	FLAVIN-ADENINE DINUCLEOTIDE	112
NImetal	NICKEL (II) ION	106
CAmetal	CALCIUM ION	70
MGmetal	MAGNESIUM ION	68
NAmetal	SODIUM ION	54
FEmetal	FE (III) ION	38
CUmetal	COPPER (II) ION	31
MNmetal	MANGANESE (II) ION	28
PXX	N-1,10-phenanthrolin-5-ylacetamide	28
COmetal	COBALT (II) ION	27
HAE	ACETOHYDROXAMIC ACID	25
3NImetal	NICKEL (III) ION	24
NO	NITRIC OXIDE	23
PCW	1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE	20
17F	O-[(S)-({(2R)-2,3-bis[(9Z)-octadec-9-enoyloxy]propyl}oxy)(hydroxy)phosphoryl]-L-serine	18
NMY	NEOMYCIN	18