X-group (possible homology)

159 all-alpha NTP pyrophosphatases

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Ligands and drugs

798

Member domains

184

with ligand contacts (≤ 4 Å)

23.1% of members

169

with DrugDomain annotations

21.2% of members

125

with a DrugBank compound

15.7% 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)

6.3

Superclasses per 20 proteins

narrower 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
Nucleosides, nucleotides, and analogues	13	6.5	1.99×	q = 0.01
Homogeneous metal compounds	21	11.6	1.81×	q = 3.4e-4
Homogeneous non-metal compounds	3	5.1	0.59×	q = 0.53
Organic salts	1	0.0	41×	not tested
Organosulfur compounds	1	0.5	2.05×	not tested
Mixed metal/non-metal compounds	1	0.5	2.01×	not tested
Organoheterocyclic compounds	1	3.6	0.28×	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
DB03800	UMP	Deoxyuridine monophosphate	30
DB01965	DUP	2'-Deoxyuridine 5'-alpha,beta-imido-triphosphate	18
DB12025	TLI	Triptolide	8
DB00118	SAM	Ademetionine	7
DB01752	SAH	S-adenosyl-L-homocysteine	7
DB03641	DUN	2'-deoxyuridine 5'-alpha,beta-imido-diphosphate	6
DB02256	DUR	2'-Deoxyuridine	4
DB03413	DUD	Deoxyuridine-5'-Diphosphate	4
DB03491	DGI	2'-Deoxyguanosine-5'-Diphosphate	4
DB00131	AMP	Adenosine phosphate	3
DB00171	ATP	ATP	2
DB03798	DCM	2'-Deoxycytidine-5'-Monophosphate	2

Most frequently bound compounds

PDB ligand	Name	Domains in contact
MGmetal	MAGNESIUM ION	68
UMP	2'-DEOXYURIDINE 5'-MONOPHOSPHATE	30
MNmetal	MANGANESE (II) ION	24
DUP	2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE	18
ZNmetal	ZINC ION	10
AUC	GOLD (I) CYANIDE ION	8
TLI	triptolide	8
NAmetal	SODIUM ION	7
SAM	S-ADENOSYLMETHIONINE	7
AMP	ADENOSINE MONOPHOSPHATE	6
DUN	2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-DIPHOSPHATE	6
GDmetal	GADOLINIUM ATOM	6
SAH	S-ADENOSYL-L-HOMOCYSTEINE	6
CAmetal	CALCIUM ION	5
CL	CHLORIDE ION	5
523	2'-DEOXY-5-METHYLCYTIDINE 5'-(TETRAHYDROGEN TRIPHOSPHATE)	4
DGI	2'-DEOXYGUANOSINE-5'-DIPHOSPHATE	4
DUD	DEOXYURIDINE-5'-DIPHOSPHATE	4
DUR	2'-DEOXYURIDINE	4
SCN	THIOCYANATE ION	3