X-group (possible homology)

205 4Fe-4S ferredoxin

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Ligands and drugs

4,957

Member domains

1,993

with ligand contacts (≤ 4 Å)

40.2% of members

1,290

with DrugDomain annotations

26.0% of members

354

with a DrugBank compound

7.1% 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)

7.8

Superclasses per 20 proteins

broader than 53% 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	33	8.2	4.01×	q < 0.0001
Benzenoids	4	5.4	0.74×	q = 0.73
Homogeneous non-metal compounds	10	15.9	0.63×	q = 0.17
Organoheterocyclic compounds	7	11.4	0.61×	q = 0.26
Homogeneous metal compounds	20	36.3	0.55×	q = 5.2e-4
Nucleosides, nucleotides, and analogues	11	20.4	0.54×	q = 0.02
Organic acids and derivatives	3	11.4	0.26×	q = 7.3e-3
Organic oxygen compounds	2	14.7	0.14×	q < 0.0001
Organohalogen compounds	2	0.2	9.49×	not tested
Mixed metal/non-metal compounds	2	1.6	1.29×	not tested
Organic nitrogen compounds	1	2.4	0.42×	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
DB03429	CDL	Tetrastearoyl cardiolipin	79
DB03426	DGD	Digalactosyl Diacyl Glycerol (Dgdg)	61
DB02832	SRM	Siroheme	48
DB04327	PEE	Phosphatidylethanolamine	43
DB03147	FAD	Flavin adenine dinucleotide	22
DB18267	HEM	Ferroheme	11
DB07349	AGA	(1S)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PENTANOYLOXY)METHYL]ETHYL OCTANOATE	8
DB00172	PRO	Proline	7
DB02078	PG5	Triglyme	7
DB03350	NCO	Cobalt hexammine ion	6
DB13075	MQ7	Menaquinone 7	6
DB00160	ALA	Alanine	4
DB02777	PLC	Diundecyl Phosphatidyl Choline	4
DB03247	FMN	Flavin mononucleotide	4
DB16833	ADP	Adenosine disphosphate	4
DB00149	LEU	Leucine	3
DB02043	LHG	1,2-Dipalmitoyl-Phosphatidyl-Glycerole	3
DB00151	CYS	Cysteine	2
DB00157	—	NADH	2
DB01957	3CH	3-Chlorophenol	2

Most frequently bound compounds

PDB ligand	Name	Domains in contact
SF4	IRON/SULFUR CLUSTER	1,970
Kmetal	POTASSIUM ION	125
F3S	FE3-S4 CLUSTER	124
PC1	1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE	106
3PE	1,2-Distearoyl-sn-glycerophosphoethanolamine	102
MGmetal	MAGNESIUM ION	76
DGD	DIGALACTOSYL DIACYL GLYCEROL (DGDG)	60
PEE	1,2-dioleoyl-sn-glycero-3-phosphoethanolamine	56
CAmetal	CALCIUM ION	52
SRM	SIROHEME	41
CL	CHLORIDE ION	40
BVQ	NORPSEUDO-B12	38
CDL	CARDIOLIPIN	38
HEM	PROTOPORPHYRIN IX CONTAINING FE	31
B12	COBALAMIN	25
NAmetal	SODIUM ION	23
ZNmetal	ZINC ION	15
FAD	FLAVIN-ADENINE DINUCLEOTIDE	13
PLX	(9R,11S)-9-({[(1S)-1-HYDROXYHEXADECYL]OXY}METHYL)-2,2-DIMETHYL-5,7,10-TRIOXA-2LAMBDA~5~-AZA-6LAMBDA~5~-PHOSPHAOCTACOSANE-6,6,11-TRIOL	11
LMG	1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE	9