X-group (possible homology)

4024 Fe-S cluster-binding domain in nickel-iron hydrogenase small subunit

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Ligands and drugs

310

Member domains

299

with ligand contacts (≤ 4 Å)

96.5% of members

219

with DrugDomain annotations

70.6% of members

with a DrugBank compound

24.2% 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)

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Superclasses per 20 proteins

fewer than 20 proteins: too few to compare at equal depth

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	3	7.7	0.39×	q = 0.04
Mixed metal/non-metal compounds	3	0.3	9.05×	not tested
Homogeneous non-metal compounds	9	3.4	2.65×	not tested
Organoheterocyclic compounds	2	2.4	0.82×	not tested
Organic acids and derivatives	1	2.4	0.41×	not tested
Organic oxygen compounds	1	3.1	0.32×	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
DB02175	MLA	Malonic acid	6
DB18267	HEM	Ferroheme	4

Most frequently bound compounds

PDB ligand	Name	Domains in contact
SF4	IRON/SULFUR CLUSTER	279
F3S	FE3-S4 CLUSTER	236
CL	CHLORIDE ION	75
MQ9	MENAQUINONE-9	16
CAmetal	CALCIUM ION	6
MLA	MALONIC ACID	6
H2S	HYDROSULFURIC ACID	4
VK3	MENADIONE	4
SOT	morpholine-4-sulfonic acid	3
35L	IRON/SULFUR CLUSTER	2
MRD	(4R)-2-METHYLPENTANE-2,4-DIOL	2
NAmetal	SODIUM ION	2
KR	KRYPTON	1
MGmetal	MAGNESIUM ION	1