X-group (possible homology)

103 RuvA-C

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Ligands and drugs

8,921

Member domains

506

with ligand contacts (≤ 4 Å)

5.7% of members

366

with DrugDomain annotations

4.1% of members

267

with a DrugBank compound

3.0% 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.

Proteins with classified ligands

Superclasses bound (of 23)

8.6

Superclasses per 20 proteins

broader than 69% 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	20	15.3	1.31×	q = 0.24
Organoheterocyclic compounds	11	8.5	1.29×	q = 0.43
Organic acids and derivatives	10	8.5	1.17×	q = 0.66
Homogeneous non-metal compounds	13	11.9	1.09×	q = 0.81
Lipids and lipid-like molecules	6	6.2	0.98×	q = 1.00
Homogeneous metal compounds	20	27.1	0.74×	q = 0.10
Organic oxygen compounds	5	11.0	0.46×	q = 0.07
Organic nitrogen compounds	2	1.8	1.14×	not tested
Benzenoids	4	4.0	0.99×	not tested
Mixed metal/non-metal compounds	1	1.2	0.86×	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
DB00171	ATP	ATP	37
DB07497	BTI	5-(hexahydro-2-oxo-1H-thieno[3,4-D]imidazol-6-yl)pentanal	37
DB02548	S6P	D-glucitol 6-phosphate	32
DB03222	DTP	dATP	30
DB00119	PYR	Pyruvic acid	27
DB02452	TTP	Thymidine 5'-triphosphate	8
DB00121	BTN	Biotin	6
DB04315	GDP	Guanosine-5'-Diphosphate	6
DB01752	SAH	S-adenosyl-L-homocysteine	5
DB16833	ADP	Adenosine disphosphate	5
DB02181	DGT	2'-Deoxyguanosine-5'-Triphosphate	4
DB02951	3PY	3-Hydroxypyruvic Acid	4
DB03940	OXM	Oxamic Acid	4
DB04555	CDP	Cytidine-5'-Diphosphate	4
DB14128	NAD	Nadide	4
DB17135	BPV	Bromopyruvate	4
DB02637	OAA	Oxaloacetate Ion	3
DB03169	HMG	(S)-Hmg-Coa	3
DB00123	LYS	Lysine	2
DB01992	COA	Coenzyme A	2

Most frequently bound compounds

PDB ligand	Name	Domains in contact
DTP	2'-DEOXYADENOSINE 5'-TRIPHOSPHATE	100
ATP	ADENOSINE-5'-TRIPHOSPHATE	78
CL	CHLORIDE ION	44
MGmetal	MAGNESIUM ION	37
PYR	PYRUVIC ACID	37
IOD	IODIDE ION	33
S6P	D-SORBITOL-6-PHOSPHATE	32
BTI	5-(HEXAHYDRO-2-OXO-1H-THIENO[3,4-D]IMIDAZOL-6-YL)PENTANAL	25
NAmetal	SODIUM ION	14
CDP	CYTIDINE-5'-DIPHOSPHATE	12
DAT	2'-DEOXYADENOSINE-5'-DIPHOSPHATE	12
ZNmetal	ZINC ION	11
ANP	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER	9
BYT	Biocytin	8
GTP	GUANOSINE-5'-TRIPHOSPHATE	8
NAD	NICOTINAMIDE-ADENINE-DINUCLEOTIDE	8
B7N	(1R)-2-{[(S)-hydroxy{[(1S,2R,3R,4S,5S,6R)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}-1-[(octadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate	7
BTN	BIOTIN	7
COA	COENZYME A	6
GDP	GUANOSINE-5'-DIPHOSPHATE	6