X-group (possible homology)

7588 NadA-like/4-hydroxy-3-methylbut-2-enyl diphosphate reductase

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Ligands and drugs

2,315

Member domains

278

with ligand contacts (≤ 4 Å)

12.0% of members

275

with DrugDomain annotations

11.9% of members

with a DrugBank compound

3.8% 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)

—

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
Organic nitrogen compounds	1	0.2	6.36×	not tested
Homogeneous non-metal compounds	4	1.1	3.77×	not tested
Lipids and lipid-like molecules	2	0.6	3.64×	not tested
Organic oxygen compounds	3	1.0	3.06×	not tested
Benzenoids	1	0.4	2.77×	not tested
Organoheterocyclic compounds	2	0.8	2.64×	not tested
Organic acids and derivatives	2	0.8	2.62×	not tested
Homogeneous metal compounds	1	2.4	0.41×	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
DB01796	NTM	Quinolinic Acid	15
DB04714	IPE	ISOPENTENYL PYROPHOSPHATE	12
DB01785	DMA	Dimethylallyl Diphosphate	6
DB01799	EIP	4-Hydroxy-3-Methyl Butyl Diphosphate	6
DB02746	PHT	Phthalic Acid	6
DB03026	PGH	Phosphoglycolohydroxamic Acid	6
DB04326	13P	Dihydroxyacetone phosphate	6
DB04299	MAE	Maleic acid	3
DB04734	CIZ	Citraconic acid	3
DB03309	NHE	N-cyclohexyltaurine	2

Most frequently bound compounds

PDB ligand	Name	Domains in contact
SF4	IRON/SULFUR CLUSTER	195
F3S	FE3-S4 CLUSTER	81
CL	CHLORIDE ION	37
H6P	(2E)-4-hydroxy-3-methylbut-2-en-1-yl trihydrogen diphosphate	30
NTM	QUINOLINIC ACID	15
0JX	(3E)-4-hydroxybut-3-en-1-yl trihydrogen diphosphate	12
10E	(2E)-4-amino-3-methylbut-2-en-1-yl trihydrogen diphosphate	12
10G	(2E)-3-methyl-4-sulfanylbut-2-en-1-yl trihydrogen diphosphate	12
IPE	3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE	12
POP	PYROPHOSPHATE 2-	12
NAmetal	SODIUM ION	7
0CG	prop-2-yn-1-yl trihydrogen diphosphate	6
0CH	4-hydroxybutyl trihydrogen diphosphate	6
0CJ	4-oxopentyl trihydrogen diphosphate	6
0CM	but-2-yn-1-yl trihydrogen diphosphate	6
0CN	buta-2,3-dien-1-yl trihydrogen diphosphate	6
0K2	4-oxobutyl trihydrogen diphosphate	6
0O3	3-(hydroxymethyl)but-3-en-1-yl trihydrogen diphosphate	6
10D	(2E)-4-fluoro-3-methylbut-2-en-1-yl trihydrogen diphosphate	6
13P	1,3-DIHYDROXYACETONEPHOSPHATE	6