X-group (possible homology)

292 RIP/Polo-box domain

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Ligands and drugs

1,045

Member domains

397

with ligand contacts (≤ 4 Å)

38.0% of members

374

with DrugDomain annotations

35.8% of members

300

with a DrugBank compound

28.7% 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.

Proteins with classified ligands

Superclasses bound (of 23)

9.6

Superclasses per 20 proteins

broader than 90% 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
Organoheterocyclic compounds	20	5.0	3.99×	q < 0.0001
Organic oxygen compounds	19	6.5	2.93×	q < 0.0001
Nucleosides, nucleotides, and analogues	7	9.0	0.78×	q = 0.64
Homogeneous non-metal compounds	5	7.0	0.71×	q = 0.60
Organic acids and derivatives	3	5.0	0.60×	q = 0.55
Homogeneous metal compounds	6	16.0	0.38×	q = 1.1e-3
Organic nitrogen compounds	5	1.0	4.82×	not tested
Hydrocarbons	1	0.2	4.40×	not tested
Phenylpropanoids and polyketides	1	0.7	1.48×	not tested
Benzenoids	2	2.4	0.84×	not tested
Lipids and lipid-like molecules	1	3.6	0.28×	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
DB00141	NAG	N-Acetylglucosamine	94
DB00173	ADE	Adenine	34
DB00131	AMP	Adenosine phosphate	7
DB02219	CXS	3-(cyclohexylamino)propanesulfonic acid	5
DB03464	FMP	Formycin-5'-Monophosphate	5
DB12010	—	Fostamatinib	5
DB02175	MLA	Malonic acid	4
DB02377	GUN	Guanine	4
DB02281	FMC	Formycin	3
DB02701	NCA	Nicotinamide	3
DB03419	URA	Uracil	3
DB00640	ADN	Adenosine	2
DB01960	M7G	7-methyl-7,8-dihydroguanosine-5'-diphosphate	2
DB01972	5GP	Guanosine-5'-Monophosphate	2
DB02527	CMP	Cyclic adenosine monophosphate	2
DB02716	MGP	7-methyl-guanosine-5'-triphosphate	2
DB04196	PT1	Pteroic acid	2
DB04357	APT	Pteric acid	2
DB04447	DTT	1,4-Dithiothreitol	2
DB11336	H35	Kinetin	2

Most frequently bound compounds

PDB ligand	Name	Domains in contact
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	98
CL	CHLORIDE ION	62
ADE	ADENINE	35
ZNmetal	ZINC ION	17
NAmetal	SODIUM ION	8
AMP	ADENOSINE MONOPHOSPHATE	7
AZI	AZIDE ION	5
CXS	3-CYCLOHEXYL-1-PROPYLSULFONIC ACID	5
FMP	FORMYCIN-5'-MONOPHOSPHATE	5
GUN	GUANINE	4
MLA	MALONIC ACID	4
NImetal	NICKEL (II) ION	4
C2X	9,9'-{(2R,3R,3aR,5S,7aR,9R,10R,10aR,12S,23R,25aR,27R,28R,28aR,30S,32aR,35aR,37S,39aR)-9-(6-amino-9H-purin-9-yl)-34-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]-5,12,23,30,37-pentahydroxy-3,10,28-trimethoxy-5,12,23,30,37-pentaoxidotetracosahydro-2H,7H,25H-trifuro[3,2-f:3',2'-l:3'',2''-x]pyrrolo[3,4-r][1,3,5,9,11,15,17,21,23,27,29,2,4,10,16,22,28]undecaoxazapentaphosphacyclopentatriacontine-2,27-diyl}bis(2-amino-3,9-dihydro-6H-purin-6-one)	3
FMC	(1S)-1-(7-amino-1H-pyrazolo[4,3-d]pyrimidin-3-yl)-1,4-anhydro-D-ribitol	3
GAL	beta-D-galactopyranose	3
MGmetal	MAGNESIUM ION	3
MY6	2-amino-7-methyl-1,7-dihydro-6H-purin-6-one	3
NCA	NICOTINAMIDE	3
URA	URACIL	3
5GP	GUANOSINE-5'-MONOPHOSPHATE	2