X-group (possible homology)

101 HTH

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Ligands and drugs

92,479

Member domains

7,377

with ligand contacts (≤ 4 Å)

8.0% of members

5,740

with DrugDomain annotations

6.2% of members

2,672

with a DrugBank compound

2.9% 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.

701

Proteins with classified ligands

Superclasses bound (of 23)

8.7

Superclasses per 20 proteins

broader than 73% 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
Phenylpropanoids and polyketides	26	14.4	1.81×	q = 8.8e-3
Homogeneous non-metal compounds	179	148.8	1.20×	q = 0.01
Mixed metal/non-metal compounds	17	14.5	1.17×	q = 0.58
Benzenoids	57	50.5	1.13×	q = 0.42
Homogeneous metal compounds	381	339.3	1.12×	q = 3.6e-3
Organoheterocyclic compounds	64	106.4	0.60×	q < 0.0001
Lipids and lipid-like molecules	46	77.0	0.60×	q = 2.3e-4
Organic nitrogen compounds	13	22.1	0.59×	q = 0.08
Organosulfur compounds	8	14.2	0.56×	q = 0.15
Organic oxygen compounds	61	137.6	0.44×	q < 0.0001
Organic acids and derivatives	44	106.9	0.41×	q < 0.0001
Nucleosides, nucleotides, and analogues	44	191.1	0.23×	q < 0.0001
Lignans, neolignans and related compounds	3	0.5	5.82×	not tested
Organophosphorus compounds	1	0.2	4.27×	not tested
Miscellaneous inorganic compounds	2	0.5	3.88×	not tested
Alkaloids and derivatives	9	2.4	3.81×	not tested
Organic salts	2	0.7	2.78×	not tested
Organometallic compounds	2	1.0	2.03×	not tested
Hydrocarbons	1	4.8	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
DB03864	SGM	Monothioglycerol	61
DB02527	CMP	Cyclic adenosine monophosphate	39
DB00150	TRP	Tryptophan	24
DB07950	IAC	Indoleacetic acid	23
DB00118	SAM	Ademetionine	22
DB00218	MFX	Moxifloxacin	17
DB00936	SAL	Salicylic acid	17
DB01643	TMP	Thymidine monophosphate	17
DB17031	ET	Homidium	17
DB00143	GSH	Glutathione	16
DB00773	EVP	Etoposide	16
DB00130	GLN	L-Glutamine	15
DB00141	NAG	N-Acetylglucosamine	15
DB01137	LFX	Levofloxacin	15
DB16833	ADP	Adenosine disphosphate	15
DB03345	BME	Mercaptoethanol	14
DB03895	MGR	Malachite Green	14
DB03247	FMN	Flavin mononucleotide	13
DB04447	DTT	1,4-Dithiothreitol	13
DB18267	HEM	Ferroheme	13

Most frequently bound compounds

PDB ligand	Name	Domains in contact
ZNmetal	ZINC ION	1,350
MGmetal	MAGNESIUM ION	1,134
CL	CHLORIDE ION	450
NAmetal	SODIUM ION	194
OHX	osmium (III) hexammine	139
Kmetal	POTASSIUM ION	117
FES	FE2/S2 (INORGANIC) CLUSTER	116
MNmetal	MANGANESE (II) ION	103
CAmetal	CALCIUM ION	92
SGM	MONOTHIOGLYCEROL	70
NImetal	NICKEL (II) ION	66
SF4	IRON/SULFUR CLUSTER	49
UNX	UNKNOWN ATOM OR ION	46
COmetal	COBALT (II) ION	45
CMP	ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE	42
CDmetal	CADMIUM ION	40
ADP	ADENOSINE-5'-DIPHOSPHATE	35
BR	BROMIDE ION	34
C2E	9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one)	34
SPD	SPERMIDINE	31