X-group (possible homology)

129 6-phosphogluconate dehydrogenase C-terminal domain-like

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Ligands and drugs

5,342

Member domains

1,516

with ligand contacts (≤ 4 Å)

28.4% of members

1,189

with DrugDomain annotations

22.3% of members

975

with a DrugBank compound

18.3% 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.

143

Proteins with classified ligands

Superclasses bound (of 23)

8.5

Superclasses per 20 proteins

broader than 68% 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	117	39.0	3.00×	q < 0.0001
Organic acids and derivatives	30	21.8	1.38×	q = 0.10
Organic oxygen compounds	29	28.1	1.03×	q = 0.88
Lipids and lipid-like molecules	16	15.7	1.02×	q = 0.93
Homogeneous metal compounds	39	69.2	0.56×	q < 0.0001
Homogeneous non-metal compounds	17	30.4	0.56×	q = 0.01
Benzenoids	5	10.3	0.48×	q = 0.15
Organoheterocyclic compounds	10	21.7	0.46×	q = 9.7e-3
Hydrocarbons	2	1.0	2.03×	not tested
Organosulfur compounds	4	2.9	1.38×	not tested
Organic nitrogen compounds	3	4.5	0.67×	not tested
Phenylpropanoids and polyketides	1	2.9	0.34×	not tested
Mixed metal/non-metal compounds	1	3.0	0.34×	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
DB14128	NAD	Nadide	176
DB03461	NAP	Nicotinamide adenine dinucleotide phosphate	169
DB00157	NAI	NADH	141
DB02338	NDP	NADPH	96
DB01861	UPG	Uridine diphosphate glucose	63
DB01713	UDX	UDP-alpha-D-xylose	37
DB03434	MPO	3-(N-morpholino)propanesulfonic acid	28
DB03041	UGA	UDP-alpha-D-glucuronic acid	26
DB03059	CAA	Acetoacetyl-CoA	25
DB00172	PRO	Proline	22
DB02076	6PG	6-phospho-D-gluconic acid	15
DB18267	HEM	Ferroheme	15
DB03345	BME	Mercaptoethanol	13
DB03147	FAD	Flavin adenine dinucleotide	12
DB03266	PTD	Glutaral	12
DB04023	GDX	GDP-alpha-D-mannuronic acid	12
DB00135	TYR	Tyrosine	11
DB03051	TFB	(S)-2-Tetrahydrofuroic acid	10
DB03387	HIO	N-Hydroxy-N-Isopropyloxamic Acid	10
DB16833	ADP	Adenosine disphosphate	10

Most frequently bound compounds

PDB ligand	Name	Domains in contact
MGmetal	MAGNESIUM ION	332
NAP	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE	185
NAD	NICOTINAMIDE-ADENINE-DINUCLEOTIDE	161
NAI	1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE	150
NDP	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE	117
9TY	cyclopropane-1,1-dicarboxylic acid	100
CL	CHLORIDE ION	89
UPG	URIDINE-5'-DIPHOSPHATE-GLUCOSE	59
UDX	URIDINE-5'-DIPHOSPHATE-XYLOPYRANOSE	37
MPO	3[N-MORPHOLINO]PROPANE SULFONIC ACID	28
CAA	ACETOACETYL-COENZYME A	27
FAD	FLAVIN-ADENINE DINUCLEOTIDE	26
UGA	URIDINE-5'-DIPHOSPHATE-GLUCURONIC ACID	26
NAmetal	SODIUM ION	22
G8I	(2S)-2-hydroxy-3,3-dimethylbutanoic acid	21
HEM	PROTOPORPHYRIN IX CONTAINING FE	20
PRO	PROLINE	20
6PG	6-PHOSPHOGLUCONIC ACID	19
TFB	TETRAHYDROFURAN-2-CARBOXYLIC ACID	15
BME	BETA-MERCAPTOETHANOL	13