X-group (possible homology)

7525 Phosphoglycerate mutase-like

Open in classification tree →

Ligands and drugs

1,895

Member domains

544

with ligand contacts (≤ 4 Å)

28.7% of members

463

with DrugDomain annotations

24.4% of members

353

with a DrugBank compound

18.6% 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)

8.3

Superclasses per 20 proteins

broader than 64% 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
Organic oxygen compounds	26	11.4	2.28×	q < 0.0001
Organic acids and derivatives	17	8.9	1.92×	q = 0.01
Homogeneous non-metal compounds	21	12.3	1.71×	q = 0.02
Nucleosides, nucleotides, and analogues	9	15.8	0.57×	q = 0.09
Homogeneous metal compounds	14	28.1	0.50×	q = 5.5e-4
Organoheterocyclic compounds	1	8.8	0.11×	q = 3.4e-3
Lipids and lipid-like molecules	0	6.4	0	q = 5.2e-3
Mixed metal/non-metal compounds	10	1.2	8.33×	not tested
Organosulfur compounds	3	1.2	2.55×	not tested
Organic nitrogen compounds	2	1.8	1.10×	not tested
Benzenoids	3	4.2	0.72×	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
DB00141	NAG	N-Acetylglucosamine	31
DB01666	IHS	D-Myo-Inositol-Hexasulphate	21
DB04510	3PG	3-phospho-D-glyceric acid	21
DB09459	TLA	L-tartaric acid	16
DB04522	SEP	Dexfosfoserine	10
DB16833	ADP	Adenosine disphosphate	8
DB00171	ATP	ATP	6
DB02726	PGA	2-Phosphoglycolic Acid	6
DB14981	IHP	Phytic acid	6
DB00145	GLY	Glycine	5
DB03577	2BF	Alpha-Benzyl-Aminobenzyl-Phosphonic Acid	4
DB02930	AGS	Adenosine 5'-[gamma-thio]triphosphate	3
DB03345	BME	Mercaptoethanol	3
DB03390	PT3	(2R,3R)-2,3-Dihydroxy-4-oxo-4-(propylamino)butanoic acid	3
DB04137	GTP	Guanosine-5'-Triphosphate	3
DB04444	ALF	Tetrafluoroaluminate Ion	3
DB00131	AMP	Adenosine phosphate	2
DB00172	PRO	Proline	2
DB01681	BHC	Benzene Hexacarboxylic Acid	2
DB02263	G3H	D-glyceraldehyde 3-phosphate	2

Most frequently bound compounds

PDB ligand	Name	Domains in contact
CL	CHLORIDE ION	119
NAmetal	SODIUM ION	31
F6P	6-O-phosphono-beta-D-fructofuranose	30
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	29
MGmetal	MAGNESIUM ION	23
3PG	3-PHOSPHOGLYCERIC ACID	22
IHS	D-MYO-INOSITOL-HEXASULPHATE	22
TLA	L(+)-TARTARIC ACID	16
POP	PYROPHOSPHATE 2-	15
PHS	PHOSPHONIC ACID	11
SEP	PHOSPHOSERINE	10
IOD	IODIDE ION	9
ADP	ADENOSINE-5'-DIPHOSPHATE	8
IHP	INOSITOL HEXAKISPHOSPHATE	8
Kmetal	POTASSIUM ION	7
ZNmetal	ZINC ION	7
ATP	ADENOSINE-5'-TRIPHOSPHATE	6
PGA	2-PHOSPHOGLYCOLIC ACID	6
RS3	1-deoxy-1-[8-(dimethylamino)-7-methyl-2,4-dioxo-3,4-dihydrobenzo[g]pteridin-10(2H)-yl]-D-ribitol	6
WO4	TUNGSTATE(VI)ION	6