X-group (possible homology)

131 PDEase-like

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Ligands and drugs

5,363

Member domains

2,842

with ligand contacts (≤ 4 Å)

53.0% of members

2,690

with DrugDomain annotations

50.2% of members

1,030

with a DrugBank compound

19.2% 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.

101

Proteins with classified ligands

Superclasses bound (of 23)

9.4

Superclasses per 20 proteins

broader than 88% 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	84	48.9	1.72×	q < 0.0001
Benzenoids	11	7.3	1.51×	q = 0.23
Organoheterocyclic compounds	23	15.3	1.50×	q = 0.06
Nucleosides, nucleotides, and analogues	38	27.5	1.38×	q = 0.04
Homogeneous non-metal compounds	23	21.4	1.07×	q = 0.78
Organic acids and derivatives	13	15.4	0.84×	q = 0.66
Organic oxygen compounds	14	19.8	0.71×	q = 0.23
Lipids and lipid-like molecules	2	11.1	0.18×	q = 2.9e-3
Lignans, neolignans and related compounds	1	0.1	13×	not tested
Miscellaneous inorganic compounds	1	0.1	13×	not tested
Organic 1,3-dipolar compounds	1	0.1	12×	not tested
Organic nitrogen compounds	7	3.2	2.20×	not tested
Phenylpropanoids and polyketides	3	2.1	1.45×	not tested
Organosulfur compounds	2	2.1	0.98×	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
DB04137	GTP	Guanosine-5'-Triphosphate	164
DB03222	DTP	dATP	126
DB02181	DGT	2'-Deoxyguanosine-5'-Triphosphate	117
DB07954	IBM	3-isobutyl-1-methyl-7H-xanthine	43
DB00536	GAI	Guanidine	38
DB03258	DCP	2'-Deoxycytidine 5'-triphosphate	30
DB02452	TTP	Thymidine 5'-triphosphate	26
DB00131	AMP	Adenosine phosphate	24
DB04149	ROL	(R)-Rolipram	22
DB16833	ADP	Adenosine disphosphate	17
DB00145	GLY	Glycine	16
DB02918	ZAR	Zardaverine	14
DB02431	CTP	Cytidine-5'-Triphosphate	13
DB00171	ATP	ATP	11
DB00203	VIA	Sildenafil	10
DB00139	SIN	Succinic acid	8
DB01656	ROF	Roflumilast	8
DB01791	PIL	Piclamilast	8
DB04447	DTT	1,4-Dithiothreitol	8
DB00862	VDN	Vardenafil	7

Most frequently bound compounds

PDB ligand	Name	Domains in contact
MGmetal	MAGNESIUM ION	2,234
ZNmetal	ZINC ION	2,014
FEmetal	FE (III) ION	203
GTP	GUANOSINE-5'-TRIPHOSPHATE	194
DTP	2'-DEOXYADENOSINE 5'-TRIPHOSPHATE	150
MNmetal	MANGANESE (II) ION	120
DGT	2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE	117
NImetal	NICKEL (II) ION	95
CL	CHLORIDE ION	56
IBM	3-ISOBUTYL-1-METHYLXANTHINE	46
DCP	2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE	42
GAI	GUANIDINE	38
NAmetal	SODIUM ION	32
CAmetal	CALCIUM ION	28
TTP	THYMIDINE-5'-TRIPHOSPHATE	26
AMP	ADENOSINE MONOPHOSPHATE	23
CZF	[[(2~{R},3~{S},4~{R},5~{R})-5-[2,6-bis(oxidanylidene)-3~{H}-purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate	22
ROL	ROLIPRAM	22
T8T	2'-deoxyguanosine-5'-O-(1-thiotriphosphate)	22
ADP	ADENOSINE-5'-DIPHOSPHATE	19