X-group (possible homology)

2006 HAD domain-like

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Ligands and drugs

18,638

Member domains

4,687

with ligand contacts (≤ 4 Å)

25.1% of members

4,061

with DrugDomain annotations

21.8% of members

2,142

with a DrugBank compound

11.5% 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.

405

Proteins with classified ligands

Superclasses bound (of 23)

9.7

Superclasses per 20 proteins

broader than 91% 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
Mixed metal/non-metal compounds	50	8.4	5.96×	q < 0.0001
Homogeneous metal compounds	365	196.0	1.86×	q < 0.0001
Organosulfur compounds	13	8.2	1.58×	q = 0.15
Organic nitrogen compounds	17	12.7	1.33×	q = 0.32
Homogeneous non-metal compounds	106	86.0	1.23×	q = 0.03
Phenylpropanoids and polyketides	8	8.3	0.96×	q = 1.00
Benzenoids	24	29.2	0.82×	q = 0.46
Organic oxygen compounds	59	79.5	0.74×	q = 0.02
Organic acids and derivatives	44	61.8	0.71×	q = 0.02
Organoheterocyclic compounds	40	61.5	0.65×	q = 4.8e-3
Nucleosides, nucleotides, and analogues	55	110.4	0.50×	q < 0.0001
Lipids and lipid-like molecules	12	44.5	0.27×	q < 0.0001
Lignans, neolignans and related compounds	3	0.3	10×	not tested
Organohalogen compounds	6	1.1	5.28×	not tested
Miscellaneous inorganic compounds	1	0.3	3.36×	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	89
DB04444	ALF	Tetrafluoroaluminate Ion	66
DB02565	B3N	4-(dimethylamino)-N-[7-(hydroxyamino)-7-oxoheptyl]benzamide	53
DB03909	ACP	Adenosine-5'-[Beta, Gamma-Methylene]Triphosphate	51
DB00129	ORN	Ornithine	44
DB03345	BME	Mercaptoethanol	42
DB02546	SHH	Vorinostat	33
DB01983	ABH	2(S)-Amino-6-Boronohexanoic Acid	29
DB00536	GAI	Guanidine	27
DB04297	TSN	Trichostatin A	27
DB03309	NHE	N-cyclohexyltaurine	25
DB16833	ADP	Adenosine disphosphate	22
DB03731	S2C	S-2-(Boronoethyl)-L-Cysteine	21
DB00123	LYS	Lysine	17
DB00171	ATP	ATP	16
DB00218	MFX	Moxifloxacin	15
DB00773	EVP	Etoposide	15
DB01137	LFX	Levofloxacin	15
DB14981	IHP	Phytic acid	15
DB00131	AMP	Adenosine phosphate	14

Most frequently bound compounds

PDB ligand	Name	Domains in contact
MGmetal	MAGNESIUM ION	1,664
ZNmetal	ZINC ION	1,004
MNmetal	MANGANESE (II) ION	892
Kmetal	POTASSIUM ION	760
CAmetal	CALCIUM ION	484
CL	CHLORIDE ION	426
NAmetal	SODIUM ION	408
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	113
ALF	TETRAFLUOROALUMINATE ION	100
BEF	BERYLLIUM TRIFLUORIDE ION	88
ACP	PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER	58
B3N	4-(dimethylamino)-N-[7-(hydroxyamino)-7-oxoheptyl]benzamide	53
ORN	L-ornithine	48
BME	BETA-MERCAPTOETHANOL	42
MF4	TETRAFLUOROMAGNESATE(2-)	41
NImetal	NICKEL (II) ION	40
ADP	ADENOSINE-5'-DIPHOSPHATE	39
COmetal	COBALT (II) ION	37
SHH	OCTANEDIOIC ACID HYDROXYAMIDE PHENYLAMIDE	35
ABH	2(S)-AMINO-6-BORONOHEXANOIC ACID	29