X-group (possible homology)

2 OB-fold

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Ligands and drugs

46,026

Member domains

5,229

with ligand contacts (≤ 4 Å)

11.4% of members

3,117

with DrugDomain annotations

6.8% of members

1,255

with a DrugBank compound

2.7% 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.

301

Proteins with classified ligands

Superclasses bound (of 23)

7.0

Superclasses per 20 proteins

narrower than 59% 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
Mixed metal/non-metal compounds	9	6.2	1.44×	q = 0.29
Homogeneous metal compounds	190	145.7	1.30×	q < 0.0001
Organic nitrogen compounds	10	9.5	1.06×	q = 0.91
Homogeneous non-metal compounds	67	63.9	1.05×	q = 0.74
Organic oxygen compounds	36	59.1	0.61×	q = 1.2e-3
Organic acids and derivatives	22	45.9	0.48×	q = 1.2e-4
Nucleosides, nucleotides, and analogues	31	82.0	0.38×	q < 0.0001
Organosulfur compounds	2	6.1	0.33×	q = 0.15
Phenylpropanoids and polyketides	2	6.2	0.32×	q = 0.15
Organoheterocyclic compounds	12	45.7	0.26×	q < 0.0001
Benzenoids	4	21.7	0.18×	q < 0.0001
Lipids and lipid-like molecules	5	33.0	0.15×	q < 0.0001
Organometallic compounds	1	0.4	2.37×	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
DB04205	THP	Thymidine-3',5'-Diphosphate	215
DB03709	BCN	Bicine	70
DB04473	FUC	alpha-L-fucose	49
DB15878	MOO	Molybdate	30
DB03721	SIA	N-acetyl-alpha-neuraminic acid	28
DB14128	NAD	Nadide	25
DB16833	ADP	Adenosine disphosphate	17
DB00171	ATP	ATP	16
DB01082	SRY	Streptomycin	16
DB02213	GAA	Metanitrophenyl-Alpha-D-Galactoside	15
DB03566	SPD	Spermidine	13
DB03283	FUL	beta-L-fucose	10
DB03446	AI1	N-Benzyl-3-(alpha-D-galactopyranosyloxy)benzamide	10
DB00160	ALA	Alanine	9
DB02219	CXS	3-(cyclohexylamino)propanesulfonic acid	8
DB09419	XLS	Xylose	7
DB00128	ASP	Aspartic acid	6
DB03421	I06	2-Phenethyl-2,3-Dihydro-Phthalazine-1,4-Dione	6
DB01643	TMP	Thymidine monophosphate	5
DB01992	COA	Coenzyme A	5

Most frequently bound compounds

PDB ligand	Name	Domains in contact
MGmetal	MAGNESIUM ION	2,763
CAmetal	CALCIUM ION	382
Kmetal	POTASSIUM ION	229
THP	THYMIDINE-3',5'-DIPHOSPHATE	222
CL	CHLORIDE ION	217
ZNmetal	ZINC ION	198
OHX	osmium (III) hexammine	178
NAmetal	SODIUM ION	110
GAL	beta-D-galactopyranose	77
BCN	BICINE	70
ADP	ADENOSINE-5'-DIPHOSPHATE	59
ATP	ADENOSINE-5'-TRIPHOSPHATE	56
UNX	UNKNOWN ATOM OR ION	52
MNmetal	MANGANESE (II) ION	50
WO4	TUNGSTATE(VI)ION	47
MOO	MOLYBDATE ION	42
1PS	3-PYRIDINIUM-1-YLPROPANE-1-SULFONATE	39
GLA	alpha-D-galactopyranose	36
POP	PYROPHOSPHATE 2-	35
NAD	NICOTINAMIDE-ADENINE-DINUCLEOTIDE	31