X-group (possible homology)

206 Protein kinase/SAICAR synthase/ATP-grasp

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Ligands and drugs

38,148

Member domains

13,808

with ligand contacts (≤ 4 Å)

36.2% of members

12,185

with DrugDomain annotations

31.9% of members

7,305

with a DrugBank compound

19.1% 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.

756

Proteins with classified ligands

Superclasses bound (of 23)

10.2

Superclasses per 20 proteins

broader than 96% 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
Benzenoids	195	54.5	3.58×	q < 0.0001
Phenylpropanoids and polyketides	54	15.5	3.48×	q < 0.0001
Organoheterocyclic compounds	351	114.7	3.06×	q < 0.0001
Nucleosides, nucleotides, and analogues	481	206.1	2.33×	q < 0.0001
Organosulfur compounds	33	15.3	2.15×	q = 2.1e-4
Organic nitrogen compounds	48	23.8	2.02×	q < 0.0001
Homogeneous metal compounds	410	365.9	1.12×	q = 2.9e-3
Homogeneous non-metal compounds	179	160.4	1.12×	q = 0.14
Organic acids and derivatives	124	115.3	1.07×	q = 0.46
Organic oxygen compounds	150	148.4	1.01×	q = 0.93
Mixed metal/non-metal compounds	15	15.7	0.96×	q = 1.00
Hydrocarbons	2	5.2	0.38×	q = 0.25
Lipids and lipid-like molecules	22	83.0	0.27×	q < 0.0001
Organic 1,3-dipolar compounds	2	0.6	3.21×	not tested
Hydrocarbon derivatives	2	0.6	3.12×	not tested
Miscellaneous inorganic compounds	1	0.6	1.80×	not tested
Alkaloids and derivatives	4	2.5	1.57×	not tested
Organohalogen compounds	3	2.1	1.41×	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	752
DB00171	ATP	ATP	406
DB03909	ACP	Adenosine-5'-[Beta, Gamma-Methylene]Triphosphate	338
DB12010	—	Fostamatinib	286
DB00131	AMP	Adenosine phosphate	191
DB02010	STU	Staurosporine	124
DB02930	AGS	Adenosine 5'-[gamma-thio]triphosphate	69
DB01172	KAN	Kanamycin	61
DB02082	GNP	Phosphoaminophosphonic acid guanylate ester	61
DB01254	1N1	Dasatinib	48
DB00619	STI	Imatinib	46
DB00640	ADN	Adenosine	43
DB04447	DTT	1,4-Dithiothreitol	38
DB00129	ORN	Ornithine	35
DB08901	0LI	Ponatinib	35
DB01786	DAL	D-Alanine	33
DB04315	GDP	Guanosine-5'-Diphosphate	33
DB09459	TLA	L-tartaric acid	33
DB03345	BME	Mercaptoethanol	32
DB18051	LDN	LDN-193189	32

Most frequently bound compounds

PDB ligand	Name	Domains in contact
MGmetal	MAGNESIUM ION	1,971
CL	CHLORIDE ION	1,083
ADP	ADENOSINE-5'-DIPHOSPHATE	913
ANP	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER	723
ATP	ADENOSINE-5'-TRIPHOSPHATE	515
ACP	PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER	378
NAmetal	SODIUM ION	303
AMP	ADENOSINE MONOPHOSPHATE	231
MNmetal	MANGANESE (II) ION	215
CAmetal	CALCIUM ION	187
ZNmetal	ZINC ION	172
STU	STAUROSPORINE	132
Kmetal	POTASSIUM ION	116
AGS	PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER	100
LU8	4-methyl-3-[4-(1-methylpiperidin-4-yl)phenyl]-5-(3,4,5-trimethoxyphenyl)pyridine	90
IOD	IODIDE ION	69
GNP	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER	62
KAN	KANAMYCIN A	61
STI	4-(4-METHYL-PIPERAZIN-1-YLMETHYL)-N-[4-METHYL-3-(4-PYRIDIN-3-YL-PYRIMIDIN-2-YLAMINO)-PHENYL]-BENZAMIDE	46
ADN	ADENOSINE	41