X-group (possible homology)

7533 Phosphoglycerate kinase domain 2

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Ligands and drugs

872

Member domains

with ligand contacts (≤ 4 Å)

8.8% of members

with DrugDomain annotations

8.4% of members

with a DrugBank compound

7.3% 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	10	8.2	1.22×	q = 0.55
Mixed metal/non-metal compounds	1	0.4	2.84×	not tested
Organic oxygen compounds	9	3.3	2.70×	not tested
Nucleosides, nucleotides, and analogues	11	4.6	2.37×	not tested
Organoheterocyclic compounds	3	2.6	1.16×	not tested
Homogeneous non-metal compounds	3	3.6	0.83×	not tested
Organic acids and derivatives	1	2.6	0.39×	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	35
DB16833	ADP	Adenosine disphosphate	24
DB00171	ATP	ATP	5
DB00131	AMP	Adenosine phosphate	4
DB04444	ALF	Tetrafluoroaluminate Ion	4
DB03909	ACP	Adenosine-5'-[Beta, Gamma-Methylene]Triphosphate	3
DB04555	CDP	Cytidine-5'-Diphosphate	2
DB09130	—	—	1
DB11638	—	—	1

Most frequently bound compounds

PDB ligand	Name	Domains in contact
MGmetal	MAGNESIUM ION	31
ADP	ADENOSINE-5'-DIPHOSPHATE	25
3PG	3-PHOSPHOGLYCERIC ACID	22
CL	CHLORIDE ION	10
ATP	ADENOSINE-5'-TRIPHOSPHATE	7
NAmetal	SODIUM ION	5
ALF	TETRAFLUOROALUMINATE ION	4
AMP	ADENOSINE MONOPHOSPHATE	4
ACP	PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER	3
Kmetal	POTASSIUM ION	3
LA8	L-ADENOSINE-5'-DIPHOSPHATE	3
X15	1,3-BISPHOSPHOGLYCERIC ACID	3
ANP	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER	2
BR	BROMIDE ION	2
CDP	CYTIDINE-5'-DIPHOSPHATE	2
MGF	TRIFLUOROMAGNESATE	2
OTQ	(2~{S})-2-(5-nitrofuran-2-yl)-2,3,5,6,7,8-hexahydro-1~{H}-[1]benzothiolo[2,3-d]pyrimidin-4-one	2
TZN	[4-(4-amino-6,7-dimethoxyquinazolin-2-yl)piperazin-1-yl][(2R)-tetrahydrofuran-2-yl]methanone	2
93T	3-[2-(4-bromophenyl)-5,7-dimethyl-pyrazolo[1,5-a]pyrimidin-6-yl]propanoic acid	1
AF3	ALUMINUM FLUORIDE	1