X-group (possible homology)

2005 HUP domain-like

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Ligands and drugs

18,286

Member domains

2,199

with ligand contacts (≤ 4 Å)

12.0% of members

1,892

with DrugDomain annotations

10.3% of members

1,564

with a DrugBank compound

8.6% 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.

284

Proteins with classified ligands

Superclasses bound (of 23)

8.2

Superclasses per 20 proteins

broader than 61% 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	179	77.4	2.31×	q < 0.0001
Organic acids and derivatives	81	43.3	1.87×	q < 0.0001
Organoheterocyclic compounds	50	43.1	1.16×	q = 0.32
Homogeneous non-metal compounds	65	60.3	1.08×	q = 0.59
Organosulfur compounds	6	5.8	1.04×	q = 0.88
Benzenoids	20	20.5	0.98×	q = 1.00
Homogeneous metal compounds	100	137.5	0.73×	q < 0.0001
Organic nitrogen compounds	6	8.9	0.67×	q = 0.47
Phenylpropanoids and polyketides	3	5.8	0.52×	q = 0.37
Lipids and lipid-like molecules	11	31.2	0.35×	q < 0.0001
Organic oxygen compounds	19	55.8	0.34×	q < 0.0001
Mixed metal/non-metal compounds	1	5.9	0.17×	q = 0.06
Carbides	1	0.0	158×	not tested
Organohalogen compounds	1	0.8	1.25×	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	157
DB00131	AMP	Adenosine phosphate	139
DB00150	TRP	Tryptophan	63
DB03147	FAD	Flavin adenine dinucleotide	54
DB00134	MET	Methionine	52
DB04099	DND	Deamido-Nad+	52
DB02596	APC	alpha,beta-Methyleneadenosine 5'-triphosphate	41
DB14128	NAD	Nadide	41
DB01992	COA	Coenzyme A	34
DB01831	TYM	Tryptophanyl-5'amp	27
DB03708	ADX	Adenosine 5'-phosphosulfate	27
DB00135	TYR	Tyrosine	21
DB03461	NAP	Nicotinamide adenine dinucleotide phosphate	21
DB00125	ARG	Arginine	20
DB03912	PNS	D-pantetheine 4'-phosphate	19
DB03170	COD	Dephospho Coenzyme A	18
DB12153	CDC	Citicoline	18
DB16833	ADP	Adenosine disphosphate	17
DB03227	NMN	Nicotinamide Mononucleotide	16
DB00142	GLU	Glutamic acid	15

Most frequently bound compounds

PDB ligand	Name	Domains in contact
ATP	ADENOSINE-5'-TRIPHOSPHATE	183
MGmetal	MAGNESIUM ION	155
AMP	ADENOSINE MONOPHOSPHATE	146
CL	CHLORIDE ION	137
ZNmetal	ZINC ION	78
NAmetal	SODIUM ION	68
TRP	TRYPTOPHAN	64
POP	PYROPHOSPHATE 2-	56
MET	METHIONINE	53
FAD	FLAVIN-ADENINE DINUCLEOTIDE	46
NAD	NICOTINAMIDE-ADENINE-DINUCLEOTIDE	46
SF4	IRON/SULFUR CLUSTER	45
APC	DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER	41
ANP	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER	37
PAE	PHOSPHONOACETIC ACID	36
COA	COENZYME A	34
CAmetal	CALCIUM ION	33
TYM	TRYPTOPHANYL-5'AMP	32
ADX	ADENOSINE-5'-PHOSPHOSULFATE	31
DND	NICOTINIC ACID ADENINE DINUCLEOTIDE	29