X-group (possible homology)

7574 Thiamin diphosphate-binding fold (THDP-binding)

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Ligands and drugs

6,880

Member domains

2,706

with ligand contacts (≤ 4 Å)

39.3% of members

2,352

with DrugDomain annotations

34.2% of members

1,061

with a DrugBank compound

15.4% 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.

104

Proteins with classified ligands

Superclasses bound (of 23)

8.6

Superclasses per 20 proteins

broader than 68% 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	90	15.8	5.70×	q < 0.0001
Organic oxygen compounds	39	20.4	1.91×	q = 1.0e-4
Homogeneous metal compounds	92	50.3	1.83×	q < 0.0001
Organic acids and derivatives	26	15.9	1.64×	q = 0.02
Lipids and lipid-like molecules	12	11.4	1.05×	q = 0.92
Homogeneous non-metal compounds	21	22.1	0.95×	q = 0.94
Benzenoids	7	7.5	0.93×	q = 1.00
Nucleosides, nucleotides, and analogues	24	28.4	0.85×	q = 0.46
Organic nitrogen compounds	5	3.3	1.53×	not tested
Organosulfur compounds	1	2.1	0.47×	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
DB03147	FAD	Flavin adenine dinucleotide	340
DB16833	ADP	Adenosine disphosphate	64
DB02410	HTL	2-Acetyl-3-[(4-Amino-2-Methyl-5-Pyrimidinyl)Methyl]-4-Methyl-5-(4,6,6-Trihydroxy-3,5-Dioxa-4,6-Diphosphahex-1-Yl)Thiazolium Inner Salt P,P'-Dioxide	52
DB00119	PYR	Pyruvic acid	50
DB02280	RMN	(R)-Mandelic acid	32
DB03309	NHE	N-cyclohexyltaurine	18
DB01819	PEP	Phosphoenolpyruvate	16
DB09157	CO2	Carbon dioxide	15
DB03937	E4P	D-erythrose 4-phosphate	14
DB01992	COA	Coenzyme A	12
DB04447	DTT	1,4-Dithiothreitol	11
DB03361	HE3	2-{(9as)-9a-[(1s)-1-Hydroxyethyl]-2,7-Dimethyl-9a,10-Dihydro-5h-Pyrimido[4,5-D][1,3]Thiazolo[3,2-a]Pyrimidin-8-Yl}Ethyl Trihydrogen Diphosphate	10
DB01798	P22	Ethyl Dihydrogen Diphosphate	9
DB00131	AMP	Adenosine phosphate	8
DB00161	VAL	Valine	8
DB02372	PYD	2,5-Dimethylpyrimidin-4-Amine	8
DB08689	UQ1	Ubiquinone Q1	8
DB14556	F50	Peracetic acid	8
DB00139	SIN	Succinic acid	7
DB02707	P25	Pentyl Trihydrogen Diphosphate	7

Most frequently bound compounds

PDB ligand	Name	Domains in contact
TPP	THIAMINE DIPHOSPHATE	1,420
MGmetal	MAGNESIUM ION	1,155
FAD	FLAVIN-ADENINE DINUCLEOTIDE	409
CAmetal	CALCIUM ION	303
Kmetal	POTASSIUM ION	152
TD6	(4S)-4-{3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-(2-{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)-4-methyl-1,3lambda~5~-thiazol-2-yl}-4-hydroxybutanoic acid	150
ADP	ADENOSINE-5'-DIPHOSPHATE	138
MNmetal	MANGANESE (II) ION	117
NAmetal	SODIUM ION	106
CL	CHLORIDE ION	88
TZD	2-{3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-4-METHYL-2-OXO-2,3-DIHYDRO-1,3-THIAZOL-5-YL}ETHYL TRIHYDROGENDIPHOSPHATE	62
SF4	IRON/SULFUR CLUSTER	61
PYR	PYRUVIC ACID	54
TPW	2-{4-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-3-METHYLTHIOPHEN-2-YL}ETHYL TRIHYDROGEN DIPHOSPHATE	54
HTL	2-ACETYL-THIAMINE DIPHOSPHATE	51
UQ0	2,3-DIMETHOXY-5-METHYL-1,4-BENZOQUINONE	36
ACO	ACETYL COENZYME *A	34
RMN	(R)-MANDELIC ACID	32
TDL	3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-2-(1-CARBOXY-1-HYDROXYETHYL)-5-(2-{[HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}ETHYL)-4-METHYL-1,3-THIAZOL-3-IUM	32
60G	methyl 2-[(4,6-dimethoxypyrimidin-2-yl)carbamoylsulfamoylmethyl]benzoate	29