X-group (possible homology)

141 Terpenoid synthases

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Ligands and drugs

3,907

Member domains

1,256

with ligand contacts (≤ 4 Å)

32.1% of members

1,118

with DrugDomain annotations

28.6% of members

727

with a DrugBank compound

18.6% 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.

103

Proteins with classified ligands

Superclasses bound (of 23)

8.7

Superclasses per 20 proteins

broader than 72% 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	65	11.3	5.75×	q < 0.0001
Benzenoids	17	7.4	2.29×	q = 3.6e-3
Homogeneous non-metal compounds	42	21.9	1.92×	q < 0.0001
Organic acids and derivatives	30	15.7	1.91×	q = 8.3e-4
Homogeneous metal compounds	79	49.9	1.58×	q < 0.0001
Organoheterocyclic compounds	19	15.6	1.22×	q = 0.41
Organic oxygen compounds	15	20.2	0.74×	q = 0.28
Nucleosides, nucleotides, and analogues	0	28.1	0	q < 0.0001
Organometallic compounds	1	0.1	6.91×	not tested
Organic nitrogen compounds	9	3.2	2.78×	not tested
Organosulfur compounds	5	2.1	2.39×	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
DB04714	IPE	ISOPENTENYL PYROPHOSPHATE	85
DB04695	FPS	Farnesyl thiopyrophosphate	43
DB00399	ZOL	Zoledronic acid	42
DB02552	GPP	Geranyl Diphosphate	34
DB04160	PPV	Pyrophosphoric acid	28
DB03345	BME	Mercaptoethanol	26
DB00884	RIS	Risedronic acid	23
DB01785	DMA	Dimethylallyl Diphosphate	23
DB07780	FPP	Farnesyl diphosphate	22
DB00282	210	Pamidronic acid	13
DB02508	IPR	Isopentyl Pyrophosphate	13
DB00710	BFQ	Ibandronate	10
DB04702	GST	S-[(2E)-3,7-DIMETHYLOCTA-2,6-DIENYL] TRIHYDROGENTHIODIPHOSPHATE	10
DB02270	DST	Dimethylallyl S-Thiolodiphosphate	9
DB02451	BNG	B-nonylglucoside	8
DB06548	M0N	Minodronic acid	8
DB00630	212	Alendronic acid	7
DB02099	SAZ	S-azabisabolene	7
DB07420	B65	(1R)-4-(3-phenoxyphenyl)-1-phosphonobutane-1-sulfonic acid	7
DB04242	PHB	4-hydroxybenzoic acid	6

Most frequently bound compounds

PDB ligand	Name	Domains in contact
MGmetal	MAGNESIUM ION	639
POP	PYROPHOSPHATE 2-	106
IPE	3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE	80
CL	CHLORIDE ION	53
ZNmetal	ZINC ION	51
FPS	S-[(2E,6E)-3,7,11-TRIMETHYLDODECA-2,6,10-TRIENYL] TRIHYDROGEN THIODIPHOSPHATE	48
ZOL	ZOLEDRONIC ACID	44
BTM	N-benzyl-N,N-diethylethanaminium	38
NAmetal	SODIUM ION	35
PPV	PYROPHOSPHATE	35
AHD	4-AMINO-1-HYDROXYBUTANE-1,1-DIYLDIPHOSPHONATE	30
GPP	GERANYL DIPHOSPHATE	29
BME	BETA-MERCAPTOETHANOL	26
CAmetal	CALCIUM ION	26
MNmetal	MANGANESE (II) ION	25
GRG	GERANYLGERANYL DIPHOSPHATE	24
FPP	FARNESYL DIPHOSPHATE	23
RIS	1-HYDROXY-2-(3-PYRIDINYL)ETHYLIDENE BIS-PHOSPHONIC ACID	22
JF1	(1S,5S,8S,9aR)-1,9a-dimethyl-8-(prop-1-en-2-yl)octahydro-2H-quinolizinium	16
DPO	DIPHOSPHATE	14