X-group (possible homology)

5104 C-terminal domain in DHH phosphoesterases

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Ligands and drugs

1,505

Member domains

with ligand contacts (≤ 4 Å)

5.7% of members

with DrugDomain annotations

5.4% of members

with a DrugBank compound

3.5% 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)

4.0

Superclasses per 20 proteins

narrower than 89% 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
Nucleosides, nucleotides, and analogues	9	5.5	1.65×	q = 0.12
Homogeneous metal compounds	12	9.7	1.24×	q = 0.45
Homogeneous non-metal compounds	7	4.2	1.65×	not tested
Organic oxygen compounds	1	3.9	0.26×	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
DB00131	AMP	Adenosine phosphate	15
DB01972	5GP	Guanosine-5'-Monophosphate	3
DB00160	—	Alanine	2
DB01812	A3P	Adenosine 3',5'-diphosphate	2
DB02431	CTP	Cytidine-5'-Triphosphate	2
DB00171	ATP	ATP	1
DB01643	TMP	Thymidine monophosphate	1
DB03403	C5P	Cytidine-5'-Monophosphate	1

Most frequently bound compounds

PDB ligand	Name	Domains in contact
AMP	ADENOSINE MONOPHOSPHATE	12
2PN	IMIDODIPHOSPHORIC ACID	8
MGmetal	MAGNESIUM ION	8
CL	CHLORIDE ION	6
MNmetal	MANGANESE (II) ION	6
CAmetal	CALCIUM ION	4
5GP	GUANOSINE-5'-MONOPHOSPHATE	3
2BA	(2R,3R,3aS,5R,7aR,9R,10R,10aS,12R,14aR)-2,9-bis(6-amino-9H-purin-9-yl)octahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-3,5,10,12-tetrol 5,12-dioxide	2
A3P	ADENOSINE-3'-5'-DIPHOSPHATE	2
C2E	9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one)	2
CTP	CYTIDINE-5'-TRIPHOSPHATE	2
IOD	IODIDE ION	2
IY0	[5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3,4-bis(oxidanyl)furan-2-yl]methyl dihydrogen phosphate	2
IY9	[5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3-oxidanyl-furan-2-yl]methyl dihydrogen phosphate	2
A1JDM	[(2~{R},3~{R},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-fluoranyl-2-(phosphonooxymethyl)oxolan-3-yl]oxy-[2-[(2~{R},3~{S},5~{R})-5-(6-aminopurin-9-yl)-3-oxidanyl-oxolan-2-yl]ethenyl]phosphinic acid	1
ATP	ADENOSINE-5'-TRIPHOSPHATE	1
C5P	CYTIDINE-5'-MONOPHOSPHATE	1
IXK	[5-(6-aminopurin-9-yl)-2-(hydroxymethyl)furan-3-yl] [5-(6-aminopurin-9-yl)-3-oxidanyl-furan-2-yl]methyl hydrogen phosphate	1
TMP	THYMIDINE-5'-PHOSPHATE	1
ZNmetal	ZINC ION	1