X-group (possible homology)

2500 Ten stranded beta/alpha barrel

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Ligands and drugs

896

Member domains

429

with ligand contacts (≤ 4 Å)

47.9% of members

248

with DrugDomain annotations

27.7% of members

220

with a DrugBank compound

24.6% 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)

8.0

Superclasses per 20 proteins

broader than 55% 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	13	7.1	1.83×	q = 0.03
Organic oxygen compounds	6	5.1	1.18×	q = 0.70
Homogeneous metal compounds	11	12.6	0.87×	q = 0.64
Homogeneous non-metal compounds	4	5.5	0.72×	q = 0.71
Organic nitrogen compounds	2	0.8	2.45×	not tested
Benzenoids	4	1.9	2.13×	not tested
Organic acids and derivatives	8	4.0	2.02×	not tested
Organoheterocyclic compounds	4	4.0	1.01×	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
DB02452	TTP	Thymidine 5'-triphosphate	49
DB03222	DTP	dATP	48
DB04555	CDP	Cytidine-5'-Diphosphate	22
DB02181	DGT	2'-Deoxyguanosine-5'-Triphosphate	17
DB04315	GDP	Guanosine-5'-Diphosphate	17
DB00122	CHT	Choline	16
DB16833	ADP	Adenosine disphosphate	9
DB04401	BTL	Betaine aldehyde	8
DB08847	HYP	Hydroxyproline	8
DB03435	UDP	Uridine-5'-Diphosphate	7
DB00119	PYR	Pyruvic acid	5
DB03278	DTL	D-Treitol	4
DB04349	PGO	(S)-propane-1,2-diol	4
DB01677	FUM	Fumaric acid	3
DB02431	CTP	Cytidine-5'-Triphosphate	3
DB03940	OXM	Oxamic Acid	3
DB00171	ATP	ATP	2
DB00640	ADN	Adenosine	2
DB01992	COA	Coenzyme A	2
DB03258	DCP	2'-Deoxycytidine 5'-triphosphate	2

Most frequently bound compounds

PDB ligand	Name	Domains in contact
TTP	THYMIDINE-5'-TRIPHOSPHATE	148
MGmetal	MAGNESIUM ION	139
DTP	2'-DEOXYADENOSINE 5'-TRIPHOSPHATE	81
CDP	CYTIDINE-5'-DIPHOSPHATE	30
DGT	2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE	18
ZNmetal	ZINC ION	18
GDP	GUANOSINE-5'-DIPHOSPHATE	17
CHT	CHOLINE ION	16
NAmetal	SODIUM ION	12
ATP	ADENOSINE-5'-TRIPHOSPHATE	11
ADP	ADENOSINE-5'-DIPHOSPHATE	9
CL	CHLORIDE ION	9
8X3	2-hydroxyethylsulfonic acid	8
A1H9I	fluoromethylcholine	8
A1H9K	cyclopropylcholine	8
A1H9L	difluorocholine	8
BTL	BETAINE ALDEHYDE	8
FUM	FUMARIC ACID	8
HYP	4-HYDROXYPROLINE	8
ANP	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER	7