X-group (possible homology)

297 YrdC/RibB

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Ligands and drugs

807

Member domains

118

with ligand contacts (≤ 4 Å)

14.6% of members

with DrugDomain annotations

10.8% of members

with a DrugBank compound

7.3% 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	11	6.8	1.62×	q = 0.05
Organic oxygen compounds	6	2.8	2.18×	not tested
Organic acids and derivatives	4	2.1	1.87×	not tested
Nucleosides, nucleotides, and analogues	4	3.8	1.05×	not tested
Homogeneous non-metal compounds	2	3.0	0.67×	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
DB00156	THR	Threonine	11
DB04496	RES	4-Phospho-D-erythronohydroxamic acid	4
DB02596	APC	alpha,beta-Methyleneadenosine 5'-triphosphate	3
DB04034	5SP	Ribulose-5-Phosphate	3
DB00131	AMP	Adenosine phosphate	1
DB00171	ATP	ATP	1
DB01923	N3U	L-Xylulose 5-Phosphate	1
DB02053	R5P	Ribose-5-phosphate	1
DB09459	TLA	L-tartaric acid	1

Most frequently bound compounds

PDB ligand	Name	Domains in contact
MGmetal	MAGNESIUM ION	22
THR	THREONINE	15
ZNmetal	ZINC ION	14
5RP	RIBULOSE-5-PHOSPHATE	13
CP	PHOSPHORIC ACID MONO(FORMAMIDE)ESTER	12
MNmetal	MANGANESE (II) ION	9
ATP	ADENOSINE-5'-TRIPHOSPHATE	5
CAmetal	CALCIUM ION	5
DPO	DIPHOSPHATE	5
Kmetal	POTASSIUM ION	4
POP	PYROPHOSPHATE 2-	4
RES	4-PHOSPHO-D-ERYTHRONOHYDROXAMIC ACID	4
TXA	threonylcarbamoyladenylate	4
U6A	N-carboxy-L-threonine	4
5SP	5-O-phosphono-D-xylulose	3
APC	DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER	3
CL	CHLORIDE ION	3
ADP	ADENOSINE-5'-DIPHOSPHATE	2
ANP	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER	2
AUmetal	GOLD ION	2