X-group (possible homology)

2008 Restriction endonuclease-like

Open in classification tree →

Ligands and drugs

7,082

Member domains

926

with ligand contacts (≤ 4 Å)

13.1% of members

860

with DrugDomain annotations

12.1% of members

423

with a DrugBank compound

6.0% 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.

123

Proteins with classified ligands

Superclasses bound (of 23)

7.5

Superclasses per 20 proteins

narrower than 52% 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	101	59.5	1.70×	q < 0.0001
Homogeneous non-metal compounds	35	26.1	1.34×	q = 0.09
Benzenoids	9	8.9	1.01×	q = 0.91
Organoheterocyclic compounds	16	18.7	0.86×	q = 0.69
Organic oxygen compounds	14	24.2	0.58×	q = 0.04
Organic acids and derivatives	6	18.8	0.32×	q = 1.5e-3
Nucleosides, nucleotides, and analogues	8	33.5	0.24×	q < 0.0001
Lipids and lipid-like molecules	1	13.5	0.07×	q < 0.0001
Hydrocarbon derivatives	1	0.1	9.60×	not tested
Organohalogen compounds	1	0.4	2.90×	not tested
Organosulfur compounds	2	2.5	0.80×	not tested
Phenylpropanoids and polyketides	2	2.5	0.79×	not tested
Mixed metal/non-metal compounds	2	2.6	0.79×	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
DB14981	IHP	Phytic acid	21
DB15675	E4Z	Baloxavir	21
DB00171	ATP	ATP	14
DB01643	TMP	Thymidine monophosphate	10
DB03685	U5P	Uridine monophosphate	8
DB06817	RLT	Raltegravir	5
DB01672	DBH	2,3-Dihydroxy-Benzoic Acid	4
DB03345	BME	Mercaptoethanol	3
DB00131	AMP	Adenosine phosphate	2
DB00160	ALA	Alanine	2
DB01812	A3P	Adenosine 3',5'-diphosphate	2
DB02175	MLA	Malonic acid	2
DB02210	HEZ	Hexane-1,6-Diol	2
DB04119	TBR	Hexatantalum Dodecabromide	2
DB04160	PPV	Pyrophosphoric acid	2
DB09459	TLA	L-tartaric acid	2
DB00133	SER	Serine	1
DB00139	SIN	Succinic acid	1
DB00142	GLU	Glutamic acid	1
DB01992	COA	Coenzyme A	1

Most frequently bound compounds

PDB ligand	Name	Domains in contact
MNmetal	MANGANESE (II) ION	380
MGmetal	MAGNESIUM ION	176
CAmetal	CALCIUM ION	136
CL	CHLORIDE ION	56
NAmetal	SODIUM ION	48
QQ4	Hexa Vinylpyrrolidone K15	41
SF4	IRON/SULFUR CLUSTER	31
E4Z	Baloxavir acid	23
ZNmetal	ZINC ION	20
XI7	2-4-DIOXO-4-PHENYLBUTANOIC ACID	15
ATP	ADENOSINE-5'-TRIPHOSPHATE	13
0N8	(2Z)-4-[1-benzyl-4-(4-chlorobenzyl)piperidin-4-yl]-2-hydroxy-4-oxobut-2-enoic acid	10
TMP	THYMIDINE-5'-PHOSPHATE	10
MN3metal	MANGANESE (III) ION	9
U5P	URIDINE-5'-MONOPHOSPHATE	8
IHP	INOSITOL HEXAKISPHOSPHATE	7
BR	BROMIDE ION	6
A1J4F	9-oxidanyl-6-[(1-phenylcyclohexyl)methyl]-2-propan-2-yl-3,4-dihydropyrazino[1,2-c]pyrimidine-1,8-dione	5
RLT	N-(4-fluorobenzyl)-5-hydroxy-1-methyl-2-(1-methyl-1-{[(5-methyl-1,3,4-oxadiazol-2-yl)carbonyl]amino}ethyl)-6-oxo-1,6-dihydropyrimidine-4-carboxamide	5
0N7	2-hydroxyisoquinoline-1,3(2H,4H)-dione	4