X-group (possible homology)

7532 Phosphoglycerate kinase domain 1

Open in classification tree →

Ligands and drugs

871

Member domains

with ligand contacts (≤ 4 Å)

7.2% of members

with DrugDomain annotations

6.9% of members

with a DrugBank compound

6.3% 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.

Proteins with classified ligands

Superclasses bound (of 23)

—

Superclasses per 20 proteins

fewer than 20 proteins: too few to compare at equal depth

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
Homogeneous metal compounds	3	5.3	0.56×	q = 0.30
Mixed metal/non-metal compounds	1	0.2	4.39×	not tested
Organic oxygen compounds	8	2.2	3.70×	not tested
Nucleosides, nucleotides, and analogues	3	3.0	1.00×	not tested
Homogeneous non-metal compounds	2	2.3	0.86×	not tested
Organic acids and derivatives	1	1.7	0.60×	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
DB04510	3PG	3-phospho-D-glyceric acid	37
DB04444	ALF	Tetrafluoroaluminate Ion	4
DB00131	AMP	Adenosine phosphate	2
DB00171	ATP	ATP	1
DB03909	ACP	Adenosine-5'-[Beta, Gamma-Methylene]Triphosphate	1
DB09130	—	—	1
DB11638	—	—	1

Most frequently bound compounds

PDB ligand	Name	Domains in contact
3PG	3-PHOSPHOGLYCERIC ACID	37
CL	CHLORIDE ION	11
ALF	TETRAFLUOROALUMINATE ION	4
ATP	ADENOSINE-5'-TRIPHOSPHATE	3
MGmetal	MAGNESIUM ION	3
X15	1,3-BISPHOSPHOGLYCERIC ACID	3
AMP	ADENOSINE MONOPHOSPHATE	2
Kmetal	POTASSIUM ION	2
MGF	TRIFLUOROMAGNESATE	2
ACP	PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER	1
AF3	ALUMINUM FLUORIDE	1
BEF	BERYLLIUM TRIFLUORIDE ION	1
BR	BROMIDE ION	1
CAmetal	CALCIUM ION	1
NAmetal	SODIUM ION	1