ECOD
X-group (possible homology)

4964 helical bundle in Bacillus stearothermophilus-like DNA polymerase I

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Ligands and drugs

670
Member domains
367
with ligand contacts (≤ 4 Å)
54.8% of members
292
with DrugDomain annotations
43.6% of members
187
with a DrugBank compound
27.9% 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.

16
Proteins with classified ligands
8
Superclasses bound (of 23)
—
Superclasses per 20 proteins
fewer than 20 proteins: too few to compare at equal depth

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
Homogeneous metal compounds117.71.42×q = 0.19
Organic 1,3-dipolar compounds10.076×not tested
Nucleosides, nucleotides, and analogues144.43.21×not tested
Benzenoids21.21.73×not tested
Homogeneous non-metal compounds53.41.47×not tested
Organic oxygen compounds43.11.27×not tested
Organoheterocyclic compounds32.41.24×not tested
Organic acids and derivatives12.40.41×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
DB02181DGT2'-Deoxyguanosine-5'-Triphosphate33
DB03258DCP2'-Deoxycytidine 5'-triphosphate21
DB02452TTPThymidine 5'-triphosphate14
DB02189DDS2',3'-Dideoxyadenosine triphosphate12
DB02431CTPCytidine-5'-Triphosphate12
DB00171ATPATP6
DB02596APCalpha,beta-Methyleneadenosine 5'-triphosphate5
DB03222DTPdATP4
DB038963POTriphosphoric acid4
DB04137GTPGuanosine-5'-Triphosphate4
DB03152BGLB-2-Octylglucoside2
DB00131AMPAdenosine phosphate1
DB019725GPGuanosine-5'-Monophosphate1
DB03532G2PPhosphomethylphosphonic acid guanylate ester1
DB07435BAP1,2,3-TRIHYDROXY-1,2,3,4-TETRAHYDROBENZO[A]PYRENE1

Most frequently bound compounds

PDB ligandNameDomains in contact
DGT2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE40
MGmetalMAGNESIUM ION37
DG32'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE31
DCP2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE29
DPODIPHOSPHATE24
DCT2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE23
TTPTHYMIDINE-5'-TRIPHOSPHATE15
CTPCYTIDINE-5'-TRIPHOSPHATE12
DDS2',3'-dideoxyadenosine triphosphate12
DTP2'-DEOXYADENOSINE 5'-TRIPHOSPHATE12
D3T2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE11
XG42'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]guanosine9
CLCHLORIDE ION7
DAD2',3'-DIDEOXYADENOSINE-5'-TRIPHOSPHATE7
ATPADENOSINE-5'-TRIPHOSPHATE6
APCDIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER5
3POTRIPHOSPHATE4
GTPGUANOSINE-5'-TRIPHOSPHATE4
K8I(2~{S},3~{R})-1-[3-cyano-6-methyl-4-(trifluoromethyl)pyridin-2-yl]-~{N}-methyl-~{N}-(3-methylphenyl)-3-oxidanyl-pyrrolidine-2-carboxamide4
POPPYROPHOSPHATE 2-4