X-group (possible homology)

3699 Spermidine synthase tetramerisation domain

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Ligands and drugs

487

Member domains

176

with ligand contacts (≤ 4 Å)

36.1% of members

173

with DrugDomain annotations

35.5% of members

118

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)

—

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	1	5.3	0.19×	q = 0.02
Organic nitrogen compounds	9	0.4	26×	not tested
Nucleosides, nucleotides, and analogues	11	3.0	3.67×	not tested
Benzenoids	2	0.8	2.52×	not tested
Organoheterocyclic compounds	2	1.7	1.20×	not tested
Organic oxygen compounds	1	2.2	0.46×	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
DB02282	MTA	5'-S-methyl-5'-thioadenosine	68
DB02042	1PG	2-(2-{2-[2-(2-Methoxy-Ethoxy)-Ethoxy]-Ethoxy}-Ethoxy)-Ethanol	31
DB03566	SPD	Spermidine	22
DB00127	SPM	Spermine	15
DB02995	HAI	Cyclohexylammonium Ion	8
DB01917	PUT	Putrescine	6
DB02844	AAT	S-Adenosyl-1,8-Diamino-3-Thiooctane	6
DB02676	B3P	2-[3-(2-Hydroxy-1,1-Dihydroxymethyl-Ethylamino)-Propylamino]-2-Hydroxymethyl-Propane-1,3-Diol	3
DB00118	SAM	Ademetionine	2
DB00640	ADN	Adenosine	2

Most frequently bound compounds

PDB ligand	Name	Domains in contact
MTA	5'-DEOXY-5'-METHYLTHIOADENOSINE	68
S4M	5'-[(S)-(3-AMINOPROPYL)(METHYL)-LAMBDA~4~-SULFANYL]-5'-DEOXYADENOSINE	53
1PG	2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL	31
SPD	SPERMIDINE	22
SPM	SPERMINE	15
AG3	1-{4-[(3-aminopropyl)amino]butyl}guanidine	9
HAI	CYCLOHEXYLAMMONIUM ION	8
JFQ	trans-N-(3-aminopropyl)cyclohexane-1,4-diamine	7
AAT	S-ADENOSYL-1,8-DIAMINO-3-THIOOCTANE	6
PUT	1,4-DIAMINOBUTANE	6
TER	N-(3-AMINO-PROPYL)-N-(5-AMINOPROPYL)-1,4-DIAMINOBUTANE	5
4JV	5-[(4-methylbenzyl)oxy]quinazoline-2,4-diamine	4
4JW	(2S)-N-methyl-N-phenyl-2,3-dihydro-1,4-benzodioxine-2-carboxamide	4
4K2	quinolin-8-yl piperidine-1-carboxylate	4
8OF	N-(4-methoxyphenyl)quinolin-4-amine	4
8QO	5-methoxy-2-[(5R)-5-methyl-4,5-dihydro-1H-imidazol-2-yl]phenol	4
BSX	2-(2-fluorophenyl)ethanamine	4
DSH	5'-S-(3-aminopropyl)-5'-thioadenosine	4
2MH	cis-4-methylcyclohexanamine	3
4MN	4-METHYLANILINE	3