X-group (possible homology)

7534 Undecaprenyl diphosphate synthase

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Ligands and drugs

622

Member domains

217

with ligand contacts (≤ 4 Å)

34.9% of members

190

with DrugDomain annotations

30.5% of members

142

with a DrugBank compound

22.8% 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)

8.9

Superclasses per 20 proteins

broader than 79% 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
Homogeneous metal compounds	15	10.2	1.48×	q = 0.08
Nucleosides, nucleotides, and analogues	0	5.7	0	q = 4.9e-3
Hydrocarbons	1	0.1	6.91×	not tested
Lipids and lipid-like molecules	13	2.3	5.64×	not tested
Phenylpropanoids and polyketides	2	0.4	4.64×	not tested
Benzenoids	5	1.5	3.30×	not tested
Organic acids and derivatives	7	3.2	2.19×	not tested
Homogeneous non-metal compounds	8	4.5	1.79×	not tested
Organoheterocyclic compounds	4	3.2	1.25×	not tested
Organic oxygen compounds	3	4.1	0.73×	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
DB01785	DMA	Dimethylallyl Diphosphate	20
DB02270	DST	Dimethylallyl S-Thiolodiphosphate	13
DB07780	FPP	Farnesyl diphosphate	12
DB02552	GPP	Geranyl Diphosphate	10
DB04702	GST	S-[(2E)-3,7-DIMETHYLOCTA-2,6-DIENYL] TRIHYDROGENTHIODIPHOSPHATE	10
DB04714	IPE	ISOPENTENYL PYROPHOSPHATE	10
DB03796	PLM	Palmitic Acid	6
DB04695	FPS	Farnesyl thiopyrophosphate	5
DB02508	IPR	Isopentyl Pyrophosphate	4
DB07410	B29	[2-(3-DIBENZOFURAN-4-YL-PHENYL)-1-HYDROXY-1-PHOSPHONO-ETHYL]-PHOSPHONIC ACID	3
DB01681	BHC	Benzene Hexacarboxylic Acid	2
DB06735	53Q	Enclomiphene	2
DB07404	B08	BPH-608	2
DB07409	B28	(1-HYDROXY-1-PHOSPHONO-2-[1,1';4',1'']TERPHENYL-3-YL-ETHYL)-PHOSPHONIC ACID	2
DB07426	B76	[1-HYDROXY-2-(1,1':3',1''-TERPHENYL-3-YLOXY)ETHANE-1,1-DIYL]BIS(PHOSPHONIC ACID)	2
DB02423	PIS	Thiopyrophosphate	1
DB04447	DTT	1,4-Dithiothreitol	1
DB07841	BUE	Geranylgeranyl diphosphate	1

Most frequently bound compounds

PDB ligand	Name	Domains in contact
MGmetal	MAGNESIUM ION	88
IPE	3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE	24
DMA	DIMETHYLALLYL DIPHOSPHATE	22
DST	DIMETHYLALLYL S-THIOLODIPHOSPHATE	19
DPO	DIPHOSPHATE	15
GST	GERANYL S-THIOLODIPHOSPHATE	14
FPP	FARNESYL DIPHOSPHATE	13
POP	PYROPHOSPHATE 2-	13
FQ0	2-[(2E,6E)-3,7,11-trimethyldodeca-2,6,10-trienoxy]propane-1,3-diol	12
GPP	GERANYL DIPHOSPHATE	10
ISY	3-methylbut-3-enylsulfanyl(phosphonooxy)phosphinic acid	9
FPS	S-[(2E,6E)-3,7,11-TRIMETHYLDODECA-2,6,10-TRIENYL] TRIHYDROGEN THIODIPHOSPHATE	8
FQF	(2R)-3-[(2E,6E)-3,7,11-trimethyldodeca-2,6,10-trienoxy]propane-1,2-diol	8
FV3	(2S)-3-[(2E,6E)-3,7,11-trimethyldodeca-2,6,10-trienoxy]propane-1,2-diol	8
CL	CHLORIDE ION	6
PLM	PALMITIC ACID	6
O4B	1,4,7,10,13,16-HEXAOXACYCLOOCTADECANE	5
2ZW	3-(2-chlorophenyl)-5-methyl-N-[4-(propan-2-yl)phenyl]-1,2-oxazole-4-carboxamide	4
IPR	ISOPENTYL PYROPHOSPHATE	4
B29	[2-(3-DIBENZOFURAN-4-YL-PHENYL)-1-HYDROXY-1-PHOSPHONO-ETHYL]-PHOSPHONIC ACID	3