X-group (possible homology)

5069 Transmembrane heme-binding four-helical bundle

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Ligands and drugs

4,310

Member domains

810

with ligand contacts (≤ 4 Å)

18.8% of members

600

with DrugDomain annotations

13.9% of members

582

with a DrugBank compound

13.5% 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)

7.6

Superclasses per 20 proteins

narrower than 50% 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
Lipids and lipid-like molecules	52	7.0	7.40×	q < 0.0001
Organoheterocyclic compounds	34	9.7	3.50×	q < 0.0001
Organic oxygen compounds	16	12.6	1.27×	q = 0.34
Homogeneous non-metal compounds	6	13.6	0.44×	q = 0.04
Organic acids and derivatives	3	9.8	0.31×	q = 0.03
Homogeneous metal compounds	6	31.0	0.19×	q < 0.0001
Nucleosides, nucleotides, and analogues	0	17.4	0	q < 0.0001
Hydrocarbons	4	0.4	9.07×	not tested
Benzenoids	21	4.6	4.55×	not tested
Phenylpropanoids and polyketides	1	1.3	0.76×	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	501
DB03429	CDL	Tetrastearoyl cardiolipin	132
DB03047	EPH	L-Alpha-Phosphatidyl-Beta-Oleoyl-Gamma-Palmitoyl-Phosphatidylethanolamine	69
DB04327	PEE	Phosphatidylethanolamine	69
DB03317	HEC	Ferroheme C	43
DB04657	CBE	Carboxin	36
DB02133	CLA	Chlorophyll A	25
DB02686	UMQ	Undecyl-Beta-D-Maltopyranoside	23
DB02182	HEB	Hybrid Between B and C Type Hemes (Protoporphyrin Ixcontaining Fe)	22
DB06755	BCR	Beta carotene	21
DB09270	U10	Ubidecarenone	21
DB08690	UQ2	Ubiquinone Q2	19
DB03152	BGL	B-2-Octylglucoside	16
DB13075	MQ7	Menaquinone 7	15
DB01728	PEF	1,2-dihexadecanoyl-sn-glycero-3-phosphoethanolamine	14
DB04631	AT5	Atpenin A5	12
DB08689	UQ1	Ubiquinone Q1	11
DB07349	AGA	(1S)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PENTANOYLOXY)METHYL]ETHYL OCTANOATE	8
DB07778	FMX	(S)-famoxadone	8
DB09114	PCF	Colfosceril palmitate	8

Most frequently bound compounds

PDB ligand	Name	Domains in contact
HEM	PROTOPORPHYRIN IX CONTAINING FE	700
CDL	CARDIOLIPIN	261
3PE	1,2-Distearoyl-sn-glycerophosphoethanolamine	105
PEE	1,2-dioleoyl-sn-glycero-3-phosphoethanolamine	100
PC1	1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE	93
EPH	L-ALPHA-PHOSPHATIDYL-BETA-OLEOYL-GAMMA-PALMITOYL-PHOSPHATIDYLETHANOLAMINE	69
SMA	STIGMATELLIN A	61
U10	UBIQUINONE-10	60
UQ6	5-(3,7,11,15,19,23-HEXAMETHYL-TETRACOSA-2,6,10,14,18,22-HEXAENYL)-2,3-DIMETHOXY-6-METHYL-BENZENE-1,4-DIOL	51
MQ9	MENAQUINONE-9	47
UNL	Unknown ligand	42
PTY	PHOSPHATIDYLETHANOLAMINE	39
HEC	HEME C	38
CBE	2-METHYL-N-PHENYL-5,6-DIHYDRO-1,4-OXATHIINE-3-CARBOXAMIDE	37
9YF	(2R)-2-(hexadecanoyloxy)-3-{[(S)-hydroxy{[(1R,2R,3R,4R,5R,6S)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}propyl (9S)-9-methyloctadecanoate	34
LOP	(1R)-2-{[(R)-(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(DODECANOYLOXY)METHYL]ETHYL (9Z)-OCTADEC-9-ENOATE	33
CLA	CHLOROPHYLL A	32
HDD	CIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE	31
UQ	Coenzyme Q10, (2Z,6E,10Z,14E,18E,22E,26Z)-isomer	30
UMQ	UNDECYL-MALTOSIDE	29