X-group (possible homology)

7577 PLP-dependent transferases

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Ligands and drugs

11,669

Member domains

3,970

with ligand contacts (≤ 4 Å)

34.0% of members

3,656

with DrugDomain annotations

31.3% of members

3,033

with a DrugBank compound

26.0% 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.

420

Proteins with classified ligands

Superclasses bound (of 23)

7.7

Superclasses per 20 proteins

broader than 51% 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
Organoheterocyclic compounds	347	63.7	5.45×	q < 0.0001
Organic acids and derivatives	141	64.1	2.20×	q < 0.0001
Organosulfur compounds	11	8.5	1.29×	q = 0.46
Homogeneous non-metal compounds	90	89.1	1.01×	q = 0.94
Phenylpropanoids and polyketides	8	8.6	0.93×	q = 1.00
Benzenoids	20	30.3	0.66×	q = 0.09
Organic nitrogen compounds	8	13.2	0.61×	q = 0.22
Organic oxygen compounds	36	82.5	0.44×	q < 0.0001
Homogeneous metal compounds	67	203.3	0.33×	q < 0.0001
Lipids and lipid-like molecules	13	46.1	0.28×	q < 0.0001
Mixed metal/non-metal compounds	2	8.7	0.23×	q = 0.03
Nucleosides, nucleotides, and analogues	17	114.5	0.15×	q < 0.0001
Organometallic compounds	1	0.6	1.70×	not tested
Organohalogen compounds	1	1.2	0.85×	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
DB00114	PLP	Pyridoxal phosphate	1,690
DB02142	PMP	Pyridoxamine-5'-Phosphate	259
DB02824	PLG	N-Pyridoxyl-Glycine-5-Monophosphate	148
DB00145	GLY	Glycine	70
DB00133	SER	Serine	48
DB04299	MAE	Maleic acid	46
DB08845	AKG	Oxogluric acid	33
DB00151	CYS	Cysteine	32
DB00142	GLU	Glutamic acid	27
DB02530	ABU	gamma-Aminobutyric acid	26
DB04467	PDA	N-(5'-phosphopyridoxyl)-L-alanine	26
DB11596	FFO	Levoleucovorin	22
DB00160	ALA	Alanine	21
DB03345	BME	Mercaptoethanol	19
DB03553	GUA	Glutaric Acid	18
DB00134	MET	Methionine	17
DB02783	IK2	4'-Deoxy-4'-Acetylyamino-Pyridoxal-5'-Phosphate	17
DB03287	PPG	4-(2-Amino-Ethoxy)-2-[(3-Hydroxy-2-Methyl-5-Phosphonooxymethyl-Pyridin-4-Ylmethyl)-Amino]-but-3-Enoic Acid	17
DB00139	SIN	Succinic acid	16
DB04422	HCS	Homocysteine	16

Most frequently bound compounds

PDB ligand	Name	Domains in contact
PLP	PYRIDOXAL-5'-PHOSPHATE	1,780
CL	CHLORIDE ION	357
PMP	4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE	262
NAmetal	SODIUM ION	183
PLG	N-GLYCINE-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YL-METHANE]	173
Kmetal	POTASSIUM ION	129
MGmetal	MAGNESIUM ION	87
CAmetal	CALCIUM ION	79
PLR	(5-HYDROXY-4,6-DIMETHYLPYRIDIN-3-YL)METHYL DIHYDROGEN PHOSPHATE	77
GLY	GLYCINE	66
MAE	MALEIC ACID	45
SER	SERINE	45
4LM	(2E)-2-{[(1E)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]amino}but-2-enoic acid	43
PLS	[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL]-SERINE	34
AKG	2-OXOGLUTARIC ACID	28
CYS	CYSTEINE	28
FES	FE2/S2 (INORGANIC) CLUSTER	28
0JO	2-{[(E)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]amino}prop-2-enoic acid	26
ABU	GAMMA-AMINO-BUTANOIC ACID	25
FFO	N-[4-({[(6S)-2-amino-5-formyl-4-oxo-3,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)benzoyl]-L-glutamic acid	22