X-group (possible homology)

4970 "fingers" domain in bacteriophage RB69-like DNA polymerase I

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Ligands and drugs

1,144

Member domains

479

with ligand contacts (≤ 4 Å)

41.9% of members

443

with DrugDomain annotations

38.7% of members

333

with a DrugBank compound

29.1% 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)

8.3

Superclasses per 20 proteins

broader than 64% 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	28	9.0	3.11×	q < 0.0001
Organoheterocyclic compounds	9	5.0	1.80×	q = 0.13
Organic oxygen compounds	8	6.5	1.24×	q = 0.59
Homogeneous metal compounds	10	16.0	0.63×	q = 0.09
Organic acids and derivatives	3	5.0	0.60×	q = 0.55
Homogeneous non-metal compounds	4	7.0	0.57×	q = 0.36
Organic 1,3-dipolar compounds	1	0.0	37×	not tested
Phenylpropanoids and polyketides	1	0.7	1.48×	not tested
Benzenoids	1	2.4	0.42×	not tested
Lipids and lipid-like molecules	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
DB02181	DGT	2'-Deoxyguanosine-5'-Triphosphate	53
DB02452	TTP	Thymidine 5'-triphosphate	48
DB03258	DCP	2'-Deoxycytidine 5'-triphosphate	43
DB03222	DTP	dATP	40
DB00171	ATP	ATP	16
DB02431	CTP	Cytidine-5'-Triphosphate	15
DB02189	DDS	2',3'-Dideoxyadenosine triphosphate	12
DB01965	DUP	2'-Deoxyuridine 5'-alpha,beta-imido-triphosphate	9
DB04137	GTP	Guanosine-5'-Triphosphate	6
DB01972	5GP	Guanosine-5'-Monophosphate	4
DB04005	UTP	Uridine 5'-triphosphate	4
DB04160	PPV	Pyrophosphoric acid	3
DB04447	DTT	1,4-Dithiothreitol	3
DB04457	DGP	2'-Deoxyguanosine-5'-Monophosphate	3
DB03532	G2P	Phosphomethylphosphonic acid guanylate ester	2
DB17742	2ZE	Aphidicolin	2
DB00131	AMP	Adenosine phosphate	1
DB00529	PPF	Foscarnet	1
DB02596	APC	alpha,beta-Methyleneadenosine 5'-triphosphate	1
DB02883	DOC	2',3'-Dideoxycytidine-5'-Monophosphate	1

Most frequently bound compounds

PDB ligand	Name	Domains in contact
CAmetal	CALCIUM ION	86
DGT	2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE	60
TTP	THYMIDINE-5'-TRIPHOSPHATE	48
DCP	2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE	44
DTP	2'-DEOXYADENOSINE 5'-TRIPHOSPHATE	44
DG3	2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE	28
DCT	2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE	20
ATP	ADENOSINE-5'-TRIPHOSPHATE	16
MGmetal	MAGNESIUM ION	16
CTP	CYTIDINE-5'-TRIPHOSPHATE	15
D3T	2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE	14
XG4	2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]guanosine	13
CL	CHLORIDE ION	9
DUP	2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE	9
DDS	2',3'-dideoxyadenosine triphosphate	8
NAmetal	SODIUM ION	7
ZNmetal	ZINC ION	6
DAD	2',3'-DIDEOXYADENOSINE-5'-TRIPHOSPHATE	5
GTP	GUANOSINE-5'-TRIPHOSPHATE	5
UTP	URIDINE 5'-TRIPHOSPHATE	4