X-group (possible homology)

264 LigT-like

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Ligands and drugs

746

Member domains

101

with ligand contacts (≤ 4 Å)

13.5% of members

with DrugDomain annotations

11.9% of members

with a DrugBank compound

8.8% 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)

—

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.

Superclass	Proteins	Expected	Ratio	Significance
Homogeneous metal compounds	2	5.3	0.38×	q = 0.10
Organic oxygen compounds	5	2.2	2.31×	not tested
Nucleosides, nucleotides, and analogues	6	3.0	2.00×	not tested
Homogeneous non-metal compounds	4	2.3	1.71×	not tested
Organoheterocyclic compounds	1	1.7	0.60×	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
DB03461	NAP	Nicotinamide adenine dinucleotide phosphate	7
DB03685	U5P	Uridine monophosphate	4
DB00171	ATP	ATP	3
DB02098	A2P	Adenosine-2'-5'-Diphosphate	3
DB02580	PG6	Pentaglyme	3
DB00131	AMP	Adenosine phosphate	1
DB03512	UVC	Uridine-2',3'-vanadate	1
DB04205	THP	Thymidine-3',5'-Diphosphate	1
DB04315	GDP	Guanosine-5'-Diphosphate	1

Most frequently bound compounds

PDB ligand	Name	Domains in contact
CL	CHLORIDE ION	29
2AM	ADENOSINE-2'-MONOPHOSPHATE	10
NAP	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE	7
OVE	2'-O-(sulfidophosphinato)adenosine	4
U5P	URIDINE-5'-MONOPHOSPHATE	4
A2P	ADENOSINE-2'-5'-DIPHOSPHATE	3
ATP	ADENOSINE-5'-TRIPHOSPHATE	3
CAmetal	CALCIUM ION	3
PG6	1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE	3
3AM	[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-hydroxy-2-(hydroxymethyl)oxolan-3-yl] dihydrogen phosphate	2
MGmetal	MAGNESIUM ION	2
15P	POLYETHYLENE GLYCOL (N=34)	1
ACK	2',3'- cyclic AMP	1
AMP	ADENOSINE MONOPHOSPHATE	1
C5P	CYTIDINE-5'-MONOPHOSPHATE	1
GDP	GUANOSINE-5'-DIPHOSPHATE	1
HGmetal	MERCURY (II) ION	1
QQX	[(3aR,4R,6R,6aR)-4-(6-aminopurin-9-yl)-2-oxidanyl-2-sulfanylidene-3a,4,6,6a-tetrahydrofuro[3,4-d][1,3,2]dioxaphosphol-6-yl]methanol	1
QQY	[(3aR,4R,6R,6aR)-4-(6-aminopurin-9-yl)-2-oxidanylidene-2-sulfanyl-3a,4,6,6a-tetrahydrofuro[3,4-d][1,3,2]dioxaphosphol-6-yl]methanol	1
THP	THYMIDINE-3',5'-DIPHOSPHATE	1