X-group (possible homology)

4002 alpha-helical domain in dehydroquinate synthase-like enzymes

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Ligands and drugs

1,190

Member domains

252

with ligand contacts (≤ 4 Å)

21.2% of members

230

with DrugDomain annotations

19.3% of members

173

with a DrugBank compound

14.5% 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)

6.4

Superclasses per 20 proteins

narrower than 71% 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	35	11.7	2.99×	q < 0.0001
Homogeneous metal compounds	36	20.8	1.73×	q < 0.0001
Homogeneous non-metal compounds	11	9.1	1.21×	q = 0.54
Organic oxygen compounds	7	8.4	0.83×	q = 0.77
Organic acids and derivatives	2	6.6	0.30×	q = 0.09
Organoheterocyclic compounds	0	6.5	0	q = 4.5e-3
Mixed metal/non-metal compounds	1	0.9	1.12×	not tested
Benzenoids	2	3.1	0.65×	not tested
Lipids and lipid-like molecules	1	4.7	0.21×	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	87
DB02592	CRB	Carbaphosphonate	18
DB03461	NAP	Nicotinamide adenine dinucleotide phosphate	14
DB02338	NDP	NADPH	13
DB00157	NAI	NADH	9
DB16833	ADP	Adenosine disphosphate	6
DB00145	GLY	Glycine	4
DB02319	NZQ	5,6-dihydroxy-NADP	4
DB04326	13P	Dihydroxyacetone phosphate	3
DB00142	GLU	Glutamic acid	2
DB02363	ATR	2'-Monophosphoadenosine-5'-Diphosphate	2
DB04349	PGO	(S)-propane-1,2-diol	2
DB11326	BO3	Boric acid	2
DB04160	PPV	Pyrophosphoric acid	1

Most frequently bound compounds

PDB ligand	Name	Domains in contact
ZNmetal	ZINC ION	117
NAD	NICOTINAMIDE-ADENINE-DINUCLEOTIDE	93
FEmetal	FE (III) ION	41
FE2metal	FE (II) ION	32
CRB	[1R-(1ALPHA,3BETA,4ALPHA,5BETA)]-5-(PHOSPHONOMETHYL)-1,3,4-TRIHYDROXYCYCLOHEXANE-1-CARBOXYLIC ACID	18
CL	CHLORIDE ION	17
NAP	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE	14
APR	ADENOSINE-5-DIPHOSPHORIBOSE	13
NDP	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE	13
MGmetal	MAGNESIUM ION	12
NImetal	NICKEL (II) ION	11
Kmetal	POTASSIUM ION	10
COmetal	COBALT (II) ION	8
NAI	1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE	8
ADP	ADENOSINE-5'-DIPHOSPHATE	6
MNmetal	MANGANESE (II) ION	5
NAmetal	SODIUM ION	5
13P	1,3-DIHYDROXYACETONEPHOSPHATE	4
7LH	(1R,3R,4S,5R)-3-[3-[3,4-bis(oxidanyl)phenyl]propanoyloxy]-1,4,5-tris(oxidanyl)cyclohexane-1-carboxylic acid	4
E9I	2-(3,4-dimethoxyphenyl)ethanamide	4