X-group (possible homology)

3016 C-terminal domain in some PLP-dependent transferases

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Ligands and drugs

11,296

Member domains

2,849

with ligand contacts (≤ 4 Å)

25.2% of members

2,535

with DrugDomain annotations

22.4% of members

1,733

with a DrugBank compound

15.3% 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.

309

Proteins with classified ligands

Superclasses bound (of 23)

8.0

Superclasses per 20 proteins

broader than 55% 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	182	46.9	3.88×	q < 0.0001
Organic acids and derivatives	124	47.1	2.63×	q < 0.0001
Organosulfur compounds	10	6.3	1.59×	q = 0.21
Phenylpropanoids and polyketides	7	6.3	1.10×	q = 0.76
Homogeneous non-metal compounds	57	65.6	0.87×	q = 0.34
Benzenoids	19	22.3	0.85×	q = 0.66
Organic oxygen compounds	33	60.7	0.54×	q < 0.0001
Organic nitrogen compounds	5	9.7	0.51×	q = 0.20
Lipids and lipid-like molecules	11	33.9	0.32×	q < 0.0001
Homogeneous metal compounds	43	149.6	0.29×	q < 0.0001
Nucleosides, nucleotides, and analogues	15	84.2	0.18×	q < 0.0001
Mixed metal/non-metal compounds	1	6.4	0.16×	q = 0.04

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	445
DB02824	PLG	N-Pyridoxyl-Glycine-5-Monophosphate	134
DB02142	PMP	Pyridoxamine-5'-Phosphate	83
DB00145	GLY	Glycine	65
DB04299	MAE	Maleic acid	46
DB00133	SER	Serine	39
DB00151	CYS	Cysteine	24
DB04467	PDA	N-(5'-phosphopyridoxyl)-L-alanine	24
DB11596	FFO	Levoleucovorin	22
DB03345	BME	Mercaptoethanol	21
DB08845	AKG	Oxogluric acid	19
DB03287	PPG	4-(2-Amino-Ethoxy)-2-[(3-Hydroxy-2-Methyl-5-Phosphonooxymethyl-Pyridin-4-Ylmethyl)-Amino]-but-3-Enoic Acid	17
DB00142	—	Glutamic acid	15
DB03553	GUA	Glutaric Acid	14
DB00134	MET	Methionine	13
DB02328	HEN	2-[(3-Hydroxy-2-Methyl-5-Phosphonooxymethyl-Pyridin-4-Ylmethyl)-Imino]-5-Phosphono-Pent-3-Enoic Acid	13
DB03928	CCO	Carboxymethylthio-3-(3-Chlorophenyl)-1,2,4-Oxadiazol	13
DB00120	PHE	Phenylalanine	12
DB00139	SIN	Succinic acid	12
DB00160	ALA	Alanine	12

Most frequently bound compounds

PDB ligand	Name	Domains in contact
PLP	PYRIDOXAL-5'-PHOSPHATE	235
CL	CHLORIDE ION	162
PLG	N-GLYCINE-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YL-METHANE]	149
NAmetal	SODIUM ION	88
GLY	GLYCINE	65
MGmetal	MAGNESIUM ION	50
MAE	MALEIC ACID	45
SER	SERINE	42
PMP	4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE	41
4LM	(2E)-2-{[(1E)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]amino}but-2-enoic acid	40
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	39
CAmetal	CALCIUM ION	37
PLS	[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL]-SERINE	27
TVJ	[6-methyl-4-[(~{E})-(oxamoylhydrazinylidene)methyl]-5-oxidanyl-pyridin-3-yl]methyl dihydrogen phosphate	24
WBJ	(2E)-2-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)imino]but-3-enoic acid	23
BME	BETA-MERCAPTOETHANOL	22
PPG	(2E,3E)-4-(2-aminoethoxy)-2-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)imino]but-3-enoic acid	21
0JO	2-{[(E)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]amino}prop-2-enoic acid	20
PLR	(5-HYDROXY-4,6-DIMETHYLPYRIDIN-3-YL)METHYL DIHYDROGEN PHOSPHATE	20
CYS	CYSTEINE	19