X-group (possible homology)

2484 Ribonuclease H-like

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Ligands and drugs

45,999

Member domains

12,476

with ligand contacts (≤ 4 Å)

27.1% of members

9,015

with DrugDomain annotations

19.6% of members

6,429

with a DrugBank compound

14.0% 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.

491

Proteins with classified ligands

Superclasses bound (of 23)

8.9

Superclasses per 20 proteins

broader than 77% 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
Homogeneous metal compounds	383	237.6	1.61×	q < 0.0001
Mixed metal/non-metal compounds	16	10.2	1.57×	q = 0.12
Nucleosides, nucleotides, and analogues	206	133.8	1.54×	q < 0.0001
Organosulfur compounds	15	10.0	1.51×	q = 0.15
Organic nitrogen compounds	20	15.4	1.29×	q = 0.31
Organic oxygen compounds	86	96.4	0.89×	q = 0.33
Homogeneous non-metal compounds	90	104.2	0.86×	q = 0.17
Phenylpropanoids and polyketides	8	10.1	0.79×	q = 0.71
Benzenoids	26	35.4	0.73×	q = 0.16
Organoheterocyclic compounds	45	74.5	0.60×	q = 3.3e-4
Organic acids and derivatives	40	74.9	0.53×	q < 0.0001
Lipids and lipid-like molecules	8	53.9	0.15×	q < 0.0001
Miscellaneous inorganic compounds	3	0.4	8.31×	not tested
Hydrocarbon derivatives	3	0.4	7.21×	not tested
Organohalogen compounds	3	1.4	2.17×	not tested
Alkaloids and derivatives	3	1.7	1.81×	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
DB16833	ADP	Adenosine disphosphate	2,579
DB00171	ATP	ATP	896
DB00131	AMP	Adenosine phosphate	107
DB02379	BGC	Beta-D-Glucose	88
DB08080	LAB	Latrunculin B	87
DB02621	LAR	Latrunculin A	50
DB01783	PAU	Pantothenic acid	45
DB00172	PRO	Proline	32
DB08864	T27	Rilpivirine	31
DB00238	NVP	Nevirapine	29
DB02210	HEZ	Hexane-1,6-Diol	29
DB08930	DLU	Dolutegravir	29
DB04137	GTP	Guanosine-5'-Triphosphate	28
DB03222	DTP	dATP	24
DB03909	ACP	Adenosine-5'-[Beta, Gamma-Methylene]Triphosphate	24
DB01972	5GP	Guanosine-5'-Monophosphate	22
DB04315	GDP	Guanosine-5'-Diphosphate	20
DB02159	PGR	(R)-Propylene glycol	19
DB02930	AGS	Adenosine 5'-[gamma-thio]triphosphate	18
DB04122	BG6	beta-D-glucose 6-phosphate	18

Most frequently bound compounds

PDB ligand	Name	Domains in contact
MGmetal	MAGNESIUM ION	4,601
ADP	ADENOSINE-5'-DIPHOSPHATE	4,170
ATP	ADENOSINE-5'-TRIPHOSPHATE	1,071
CAmetal	CALCIUM ION	612
CL	CHLORIDE ION	542
ZNmetal	ZINC ION	493
ANP	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER	401
Kmetal	POTASSIUM ION	313
MNmetal	MANGANESE (II) ION	276
NAmetal	SODIUM ION	264
OHX	osmium (III) hexammine	125
BGC	beta-D-glucopyranose	124
GLC	alpha-D-glucopyranose	124
AMP	ADENOSINE MONOPHOSPHATE	104
LAB	LATRUNCULIN B	88
IOD	IODIDE ION	87
CDmetal	CADMIUM ION	73
BEF	BERYLLIUM TRIFLUORIDE ION	70
9UE	Jasplakinolide	67
UNX	UNKNOWN ATOM OR ION	67