ECOD
X-group (possible homology)

316 Nucleotidyltransferase-like

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Ligands and drugs

4,849
Member domains
1,287
with ligand contacts (≤ 4 Å)
26.5% of members
1,245
with DrugDomain annotations
25.7% of members
808
with a DrugBank compound
16.7% 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.

98
Proteins with classified ligands
12
Superclasses bound (of 23)
7.3
Superclasses per 20 proteins
narrower than 56% 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.

SuperclassProteinsExpected
0.25×observed / expected4×
RatioSignificance
Nucleosides, nucleotides, and analogues7326.72.73×q < 0.0001
Homogeneous metal compounds8347.41.75×q < 0.0001
Organic oxygen compounds3119.21.61×q = 9.7e-3
Homogeneous non-metal compounds3220.81.54×q = 0.02
Organoheterocyclic compounds914.90.60×q = 0.17
Organic acids and derivatives815.00.54×q = 0.08
Benzenoids27.10.28×q = 0.08
Lipids and lipid-like molecules110.80.09×q = 7.5e-4
Organic salts10.19.95×not tested
Organic nitrogen compounds23.10.65×not tested
Organosulfur compounds12.00.50×not tested
Mixed metal/non-metal compounds12.00.49×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

DrugBankPDB ligandNameDomains
DB04160PPVPyrophosphoric acid108
DB00171ATPATP66
DB02431CTPCytidine-5'-Triphosphate51
DB02596APCalpha,beta-Methyleneadenosine 5'-triphosphate48
DB04005UTPUridine 5'-triphosphate40
DB01965DUP2'-Deoxyuridine 5'-alpha,beta-imido-triphosphate39
DB02181DGT2'-Deoxyguanosine-5'-Triphosphate38
DB03258DCP2'-Deoxycytidine 5'-triphosphate38
DB02452TTPThymidine 5'-triphosphate36
DB03222DTPdATP30
DB04137GTPGuanosine-5'-Triphosphate29
DB00131AMPAdenosine phosphate18
DB00452NMYFramycetin15
DB03085GOAGlycolic acid15
DB018603ATCordycepin Triphosphate13
DB16833ADPAdenosine disphosphate13
DB00141NAGN-Acetylglucosamine12
DB019725GPGuanosine-5'-Monophosphate9
DB03798DC2'-Deoxycytidine-5'-Monophosphate9
DB04555CDPCytidine-5'-Diphosphate8

Most frequently bound compounds

PDB ligandNameDomains in contact
MGmetalMAGNESIUM ION595
NAmetalSODIUM ION186
CLCHLORIDE ION183
MNmetalMANGANESE (II) ION182
ZNmetalZINC ION167
PPVPYROPHOSPHATE108
CAmetalCALCIUM ION87
ATPADENOSINE-5'-TRIPHOSPHATE67
CTPCYTIDINE-5'-TRIPHOSPHATE52
APCDIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER48
UTPURIDINE 5'-TRIPHOSPHATE41
DUP2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE39
DCP2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE38
DGT2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE38
TTPTHYMIDINE-5'-TRIPHOSPHATE36
DTP2'-DEOXYADENOSINE 5'-TRIPHOSPHATE30
GTPGUANOSINE-5'-TRIPHOSPHATE29
DCT2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE22
8DG8-OXO-2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE20
0KX2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]cytidine19