X-group (possible homology)

148 Histone-like

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Ligands and drugs

32,704

Member domains

7,807

with ligand contacts (≤ 4 Å)

23.9% of members

4,573

with DrugDomain annotations

14.0% of members

3,623

with a DrugBank compound

11.1% 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.

302

Proteins with classified ligands

Superclasses bound (of 23)

6.2

Superclasses per 20 proteins

narrower 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
Nucleosides, nucleotides, and analogues	223	82.3	2.71×	q < 0.0001
Mixed metal/non-metal compounds	7	6.3	1.12×	q = 0.75
Homogeneous non-metal compounds	55	64.1	0.86×	q = 0.30
Homogeneous metal compounds	102	146.2	0.70×	q < 0.0001
Organic nitrogen compounds	4	9.5	0.42×	q = 0.10
Benzenoids	8	21.8	0.37×	q = 2.6e-3
Organosulfur compounds	2	6.1	0.33×	q = 0.15
Phenylpropanoids and polyketides	2	6.2	0.32×	q = 0.15
Organic acids and derivatives	11	46.1	0.24×	q < 0.0001
Organic oxygen compounds	13	59.3	0.22×	q < 0.0001
Organoheterocyclic compounds	8	45.8	0.17×	q < 0.0001
Lipids and lipid-like molecules	5	33.2	0.15×	q < 0.0001
Organophosphorus compounds	1	0.1	9.90×	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
DB16833	ADP	Adenosine disphosphate	1,450
DB00171	ATP	ATP	921
DB02930	AGS	Adenosine 5'-[gamma-thio]triphosphate	777
DB03222	DTP	dATP	51
DB03266	PTD	Glutaral	48
DB16874	JDP	CB-5083	36
DB04315	GDP	Guanosine-5'-Diphosphate	15
DB03909	ACP	Adenosine-5'-[Beta, Gamma-Methylene]Triphosphate	11
DB04137	GTP	Guanosine-5'-Triphosphate	11
DB14756	SRT	meso-Tartaric acid	8
DB00118	SAM	Ademetionine	5
DB08605	TDB	6-METHYL-2(PROPANE-1-SULFONYL)-2H-THIENO[3,2-D][1,2,3]DIAZABORININ-1-OL	5
DB12695	—	—	5
DB03709	BCN	Bicine	4
DB04786	SVR	Suramin	4
DB03126	MNT	Mant-Adp	3
DB03147	FAD	Flavin adenine dinucleotide	3
DB00127	SPM	Spermine	2
DB00173	ADE	Adenine	2
DB01860	3AT	Cordycepin Triphosphate	2

Most frequently bound compounds

PDB ligand	Name	Domains in contact
ADP	ADENOSINE-5'-DIPHOSPHATE	2,976
ATP	ADENOSINE-5'-TRIPHOSPHATE	1,959
AGS	PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER	1,226
CL	CHLORIDE ION	434
MGmetal	MAGNESIUM ION	243
ANP	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER	202
08T	[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium	172
MNmetal	MANGANESE (II) ION	138
PTD	PENTANEDIAL	59
CAmetal	CALCIUM ION	50
DTP	2'-DEOXYADENOSINE 5'-TRIPHOSPHATE	44
BEF	BERYLLIUM TRIFLUORIDE ION	43
JDP	1-[4-(benzylamino)-7,8-dihydro-5H-pyrano[4,3-d]pyrimidin-2-yl]-2-methyl-1H-indole-4-carboxamide	36
TS6	Monothiophosphate	30
XKM	3-(4-{[(4P)-5-{[(1R)-cyclohex-2-en-1-yl]sulfanyl}-4-(pyridin-3-yl)-4H-1,2,4-triazol-3-yl]methoxy}-2,6-difluorophenyl)prop-2-yn-1-yl (1-methylpiperidin-4-yl)carbamate	30
A1AC1	(3R)-N-[2-(ethylsulfanyl)phenyl]-3-(1-oxo-1,3-dihydro-2H-isoindol-2-yl)butanamide	24
Y6Y	3-[3-cyclopentylsulfanyl-5-[[3-methyl-4-(4-methylsulfonylphenyl)phenoxy]methyl]-1,2,4-triazol-4-yl]pyridine	24
GDP	GUANOSINE-5'-DIPHOSPHATE	23
PTmetal	PLATINUM (II) ION	21
A1CYL	N-(3-{[(6P)-2-(methanesulfonyl)-6-(1-methyl-1H-pyrazol-4-yl)pyrimidin-4-yl]amino}phenyl)prop-2-enamide	18