PGK2

Summary

PGK2 (phosphoglycerate kinase 2, HGNC:8898) is a protein-coding gene on chromosome 6p12.3, encoding Phosphoglycerate kinase 2 (P07205). Catalyzes the reversible conversion of 1,3-diphosphoglycerate to 3-phosphoglycerate and plays a role in glycolysis and gluconeogenesis.

This gene is intronless, arose via retrotransposition of the phosphoglycerate kinase 1 gene, and is expressed specifically in the testis. Initially assumed to be a pseudogene, the encoded protein is actually a functional phosphoglycerate kinase that catalyzes the reversible conversion of 1,3-bisphosphoglycerate to 3-phosphoglycerate, during the Embden-Meyerhof-Parnas pathway of glycolysis, in the later stages of spermatogenesis.

Source: NCBI Gene 5232 — RefSeq curated summary.

At a glance

• Gene–disease (curated): male infertility with azoospermia or oligozoospermia due to single gene mutation (Moderate, GenCC)
• Clinical variants (ClinVar): 70 total
• Druggable target: yes
• MANE Select transcript: NM_138733

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:8898
Approved symbol	PGK2
Name	phosphoglycerate kinase 2
Location	6p12.3
Locus type	gene with protein product
Status	Approved
Aliases	PGKPS, PGK-2
Ensembl gene	ENSG00000170950
Ensembl biotype	protein_coding
OMIM	172270
Entrez	5232

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000304801

RefSeq mRNA: 1 — MANE Select: NM_138733 NM_138733

CCDS: CCDS4930

Canonical transcript exons

ENST00000304801 — 1 exons

Exon	Start	End
ENSE00001167116	49785660	49787285

Expression profiles

Bgee: expression breadth broad, 51 present calls, max score 99.72.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.2481 / max 202.5372, expressed in 5 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
73928	0.2110	5
73929	0.0231	3
73927	0.0140	3

Top tissues by expression

229 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
sperm	CL:0000019	99.72	gold quality
male germ cell	CL:0000015	98.31	gold quality
left testis	UBERON:0004533	97.49	gold quality
right testis	UBERON:0004534	97.41	gold quality
testis	UBERON:0000473	94.62	gold quality
adult organism	UBERON:0007023	91.33	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	84.21	gold quality
cervix squamous epithelium	UBERON:0006922	72.62	gold quality
secondary oocyte	CL:0000655	69.30	gold quality
type B pancreatic cell	CL:0000169	65.50	gold quality
tongue squamous epithelium	UBERON:0006919	62.97	gold quality
triceps brachii	UBERON:0001509	60.89	gold quality
gluteal muscle	UBERON:0002000	60.61	gold quality
upper arm skin	UBERON:0004263	59.84	gold quality
parotid gland	UBERON:0001831	59.53	gold quality
vena cava	UBERON:0004087	59.19	gold quality
pancreatic ductal cell	CL:0002079	58.25	silver quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	57.47	gold quality
heart right ventricle	UBERON:0002080	57.44	gold quality
trabecular bone tissue	UBERON:0002483	56.79	gold quality
cartilage tissue	UBERON:0002418	56.04	gold quality
cranial nerve II	UBERON:0000941	55.49	silver quality
nasal cavity epithelium	UBERON:0005384	55.33	gold quality
myocardium	UBERON:0002349	55.15	gold quality
cervix epithelium	UBERON:0004801	54.94	gold quality
squamous epithelium	UBERON:0006914	54.90	gold quality
mammary duct	UBERON:0001765	54.88	gold quality
epithelium of mammary gland	UBERON:0003244	54.62	gold quality
tendon of biceps brachii	UBERON:0008188	54.31	gold quality
biceps brachii	UBERON:0001507	54.01	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-GEOD-134144	yes	31.07
E-ANND-3	no	1.64

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): CREM, PBX4, PKNOX1, SP3

miRNA regulators (miRDB)

15 targeting PGK2, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-146A-5P	99.96	68.93	988
HSA-MIR-146B-5P	99.96	69.13	977
HSA-MIR-7153-5P	99.94	68.89	1006
HSA-MIR-548E-5P	99.89	72.73	4486
HSA-MIR-885-5P	99.59	68.59	879
HSA-MIR-891B	99.59	69.81	1083
HSA-MIR-6749-3P	99.00	65.73	1443
HSA-MIR-4742-5P	98.89	68.41	1542
HSA-MIR-4520-3P	98.75	66.55	963
HSA-MIR-6852-3P	98.54	67.60	1468
HSA-MIR-633	98.35	69.45	1167
HSA-MIR-585-5P	97.54	69.02	955
HSA-MIR-4670-3P	97.37	68.35	1378
HSA-MIR-219B-3P	97.31	66.96	672

Literature-anchored findings (GeneRIF, showing 3)

• Data from studies in transgenic mice suggest that Pgk2 core promoter elements are required to direct demethylation of DNA and reconfiguration of nucleosomes in testis during sexual maturation and spermatogenesis. (PMID:24000349)
• Study of (Co-IP) and reverse co-immunoprecipitation (Co-IP) of CBP86-IV (TSCBP86-IV or CABYR) in human sperm cell lysate identified phosphoglycerate kinase 2 (PGK2) as interacting partner of CABYR. Protein interactions were further confirmed by yeast two-hybrid system. (PMID:30972801)
• The Germ Cell-Specific Markers ZPBP2 and PGK2 in Testicular Biopsies Can Predict the Presence as well as the Quality of Sperm in Non-obstructive Azoospermia Patients. (PMID:33507524)

Cross-species orthologs

6 orthologs

Organism	Symbol	Gene ID
danio_rerio	pgk1	ENSDARG00000054191
mus_musculus	Pgk2	ENSMUSG00000031233
rattus_norvegicus	Pgk2	ENSRNOG00000013600
drosophila_melanogaster	CG9961	FBGN0031451
drosophila_melanogaster	Pgk	FBGN0250906
caenorhabditis_elegans	pgk-1	WBGENE00020185

Paralogs (1): PGK1 (ENSG00000102144)

Protein

Protein identifiers

Phosphoglycerate kinase 2 — P07205 (reviewed: P07205)

Alternative names: Phosphoglycerate kinase, testis specific

All UniProt accessions (2): A0A140VJR3, P07205

UniProt curated annotations — full annotation on UniProt →

Function. Catalyzes the reversible conversion of 1,3-diphosphoglycerate to 3-phosphoglycerate and plays a role in glycolysis and gluconeogenesis. Essential for sperm motility and male fertility. Not required for the completion of spermatogenesis.

Subunit / interactions. Monomer.

Subcellular location. Cytoplasm.

Tissue specificity. Mainly found in round spermatids. Localized on the principle piece in the sperm (at protein level). Testis-specific. Expression significantly decreased in the testis of elderly men.

Pathway. Carbohydrate degradation; glycolysis; pyruvate from D-glyceraldehyde 3-phosphate: step 2/5.

Similarity. Belongs to the phosphoglycerate kinase family.

RefSeq proteins (1): NP_620061* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001576	Phosphoglycerate_kinase	Family
IPR015824	Phosphoglycerate_kinase_N	Homologous_superfamily
IPR015911	Phosphoglycerate_kinase_CS	Conserved_site
IPR036043	Phosphoglycerate_kinase_sf	Homologous_superfamily

Pfam: PF00162

Enzyme classification (BRENDA):

• EC 2.7.2.3 — phosphoglycerate kinase (BRENDA: 101 organisms, 152 substrates, 191 inhibitors, 375 Km, 156 kcat entries)

Substrate kinetics (BRENDA)

20 substrates with measured Km, best-characterized 15. Km ranges are aggregated across organisms/conditions.

Substrate	Km (mM)	Measurements
ATP	0.01–9.7	154
3-PHOSPHO-D-GLYCERATE	0.0022–11.9	134
ADP	0.039–7.4	31
3-PHOSPHO-D-GLYCEROYL PHOSPHATE	0.0005–5.6	15
3-PHOSPHOGLYCERATE	0.48–0.68	10
DATP	3.45	2
L-ADP	0.1–0.27	2
D-ADP	0.077	1
D-ATP	0.5	1
D-GTP	0.5	1
GTP	0.348	1
L-2’-DCTP	2.5	1
L-2’-DGTP	1	1
L-ATP	0.3	1
L-CTP	1.5	1

Catalyzed reactions (Rhea), 1 shown:

• (2R)-3-phosphoglycerate + ATP = (2R)-3-phospho-glyceroyl phosphate + ADP (RHEA:14801)

UniProt features (56 total): binding site 39, modified residue 14, initiator methionine 1, chain 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P07205-F1	96.34	0.95

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Ligand- & substrate-binding residues (39): 65; 66; 122; 123; 170; 171; 214; 214; 215; 215; 23; 215 …

Post-translational modifications (14): 2, 2, 4, 11, 48, 75, 86, 97, 131, 146, 196, 199, 267, 291

Function

Pathways and Gene Ontology

Reactome pathways

2 pathways

ID	Pathway
R-HSA-70171	Glycolysis
R-HSA-70263	Gluconeogenesis

MSigDB gene sets: 126 (showing top): GOBP_NUCLEOSIDE_DIPHOSPHATE_METABOLIC_PROCESS, GOBP_CARBOHYDRATE_DERIVATIVE_CATABOLIC_PROCESS, GOBP_MONOSACCHARIDE_CATABOLIC_PROCESS, GOBP_ORGANOPHOSPHATE_METABOLIC_PROCESS, KEGG_GLYCOLYSIS_GLUCONEOGENESIS, GOBP_MONOCARBOXYLIC_ACID_METABOLIC_PROCESS, GOBP_CARBOHYDRATE_DERIVATIVE_METABOLIC_PROCESS, GOBP_NUCLEOBASE_CONTAINING_SMALL_MOLECULE_METABOLIC_PROCESS, GOBP_GENERATION_OF_PRECURSOR_METABOLITES_AND_ENERGY, GOBP_SMALL_MOLECULE_BIOSYNTHETIC_PROCESS, chr6p12, GOBP_MONOSACCHARIDE_BIOSYNTHETIC_PROCESS, GOBP_NUCLEOSIDE_TRIPHOSPHATE_METABOLIC_PROCESS, GOBP_CILIUM_MOVEMENT, GOBP_CILIUM_OR_FLAGELLUM_DEPENDENT_CELL_MOTILITY

GO Biological Process (5): gluconeogenesis (GO:0006094), glycolytic process (GO:0006096), phosphorylation (GO:0016310), flagellated sperm motility (GO:0030317), canonical glycolysis (GO:0061621)

GO Molecular Function (8): phosphoglycerate kinase activity (GO:0004618), ATP binding (GO:0005524), ADP binding (GO:0043531), metal ion binding (GO:0046872), nucleotide binding (GO:0000166), protein binding (GO:0005515), kinase activity (GO:0016301), transferase activity (GO:0016740)

GO Cellular Component (6): nucleus (GO:0005634), cytosol (GO:0005829), sperm fibrous sheath (GO:0035686), extracellular exosome (GO:0070062), cytoplasm (GO:0005737), cilium (GO:0005929)

Reactome top-level categories

Rollup of top-1 pathways:

Category	Pathways
Glucose metabolism	2

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	3
adenyl ribonucleotide binding	2
glucose metabolic process	1
hexose biosynthetic process	1
phosphoglycerate kinase activity	1
phosphoglycerate mutase activity	1
phosphopyruvate hydratase activity	1
pyruvate kinase activity	1
pyruvate metabolic process	1
generation of precursor metabolites and energy	1
aerobic respiration	1
carbohydrate catabolic process	1
pyridine nucleotide catabolic process	1
glyceraldehyde-3-phosphate dehydrogenase [NAD(P)+] (phosphorylating) activity	1
ADP catabolic process	1
ATP metabolic process	1
nicotinamide nucleotide metabolic process	1
phosphate-containing compound metabolic process	1
cilium-dependent cell motility	1
cilium movement involved in cell motility	1
sperm motility	1
glucokinase activity	1
glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity	1
glucose catabolic process	1
glycolytic process through glucose-6-phosphate	1
kinase activity	1
phosphotransferase activity, carboxyl group as acceptor	1
purine ribonucleoside triphosphate binding	1
anion binding	1
cation binding	1
nucleoside phosphate binding	1
heterocyclic compound binding	1
binding	1
transferase activity, transferring phosphorus-containing groups	1
catalytic activity	1
intracellular membrane-bounded organelle	1
cytoplasm	1
sperm flagellum	1
extracellular vesicle	1
intracellular anatomical structure	1

Protein interactions and networks

STRING

4238 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
PGK2	GAPDH	P00354	978
PGK2	TPI1	P00938	881
PGK2	PDHA2	P29803	820
PGK2	CRISP2	P16562	813
PGK2	J3KPS3	J3KPS3	792
PGK2	GPI	P06744	773
PGK2	TALDO1	P37837	754
PGK2	PLG	P00747	742
PGK2	H6PD	O95479	710
PGK2	GAPDHS	O14556	700
PGK2	GLUD1	P00367	682
PGK2	ENO2	P09104	680
PGK2	ENO1	P06733	668
PGK2	TKT	P29401	652
PGK2	TKTL1	P51854	652

IntAct

55 interactions, top by confidence:

A	B	Type	Score
PGK2	PGK1	psi-mi:“MI:0915”(physical association)	0.690
PGK1	PGK2	psi-mi:“MI:0915”(physical association)	0.690
ZCCHC12	PGK2	psi-mi:“MI:0915”(physical association)	0.590
LRRC40	PGK2	psi-mi:“MI:0915”(physical association)	0.560
IP6K2	PGK2	psi-mi:“MI:0914”(association)	0.560
IP6K2	PGK2	psi-mi:“MI:0915”(physical association)	0.560
LRRC40	PGK2	psi-mi:“MI:0914”(association)	0.560
PGK2		psi-mi:“MI:0915”(physical association)	0.550
ZSCAN12	A2ML1	psi-mi:“MI:0914”(association)	0.530
ESR1	PGK2	psi-mi:“MI:0914”(association)	0.530
SYT1	PGK2	psi-mi:“MI:0914”(association)	0.530
SPMIP4	PGK2	psi-mi:“MI:0914”(association)	0.530
SYT3	PGK2	psi-mi:“MI:0914”(association)	0.530
SENP2	PGK2	psi-mi:“MI:0914”(association)	0.530
INTS10	PGK2	psi-mi:“MI:0914”(association)	0.530
FLCN	ZNF609	psi-mi:“MI:0914”(association)	0.530
ZNF416	PGK2	psi-mi:“MI:0914”(association)	0.530
ENTPD7	PGK2	psi-mi:“MI:0914”(association)	0.530
POF1B	PGK2	psi-mi:“MI:0915”(physical association)	0.400
ORM1	PGK2	psi-mi:“MI:0915”(physical association)	0.400
UTP15	PGK2	psi-mi:“MI:0915”(physical association)	0.400

BioGRID (86): AKR1A1 (Co-fractionation), AKR1B1 (Co-fractionation), ALDOC (Co-fractionation), ENO1 (Co-fractionation), ENO3 (Co-fractionation), PGK2 (Co-fractionation), PGK2 (Co-fractionation), PGK2 (Co-fractionation), PGK2 (Co-fractionation), PGK2 (Co-fractionation), PGK2 (Co-fractionation), PGK1 (Affinity Capture-MS), PGK2 (Affinity Capture-MS), PGK2 (Affinity Capture-MS), PGK2 (Affinity Capture-MS)

ESM2 similar proteins: A0A7G5KET3, A0ALE2, A0Q7J1, A9NHH8, B1MW69, B2ITU1, B2KC44, B8DD98, C1F1M9, C1KY97, O60101, O61471, O74233, O94123, P00560, P07205, P09188, P11977, P12783, P14228, P14828, P24590, P29405, P29406, P29407, P33161, P38667, P41756, P41757, P46273, P91427, Q01604, Q03UX8, Q14GM9, Q38Y20, Q42962, Q5NF76, Q6BLA0, Q6FKY1, Q6RI85

Diamond homologs: A0A7G5KET3, A0PYP1, A1BJZ1, A4SH15, A5A6K4, A5HYC0, A5IJ98, A5N2N8, A6LMG3, A7FQN7, A7G9Y0, A7HCN7, A7HL11, A8F5X9, A9WKE4, B0CD95, B1IDB6, B1KTJ5, B1L8B8, B3EIM1, B3EQD1, B3QLX7, B3QWD9, B4S6S2, B4SHF6, B7IDG7, B7K9Q5, B8G4H3, B9E6B4, C1F1M9, C1FQW3, C3KYR4, O00852, O00869, O00871, O00940, O02608, O02609, O52632, O60101

SIGNOR signaling

2 interactions.

A	Effect	B	Mechanism
PGK2	“down-regulates quantity”	“3-phosphonato-D-glyceroyl phosphate(4-)”	“chemical modification”
PGK2	“up-regulates quantity”	3-phosphonato-D-glycerate(3-)	“chemical modification”

Disease & clinical

Clinical variants and AI predictions

ClinVar

70 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	70
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

84 predictions. Top by Δscore:

Variant	Effect	Δscore
6:49786354:TAC:T	donor_gain	0.6400
6:49786355:ACA:A	donor_gain	0.6400
6:49786356:CAC:C	donor_gain	0.6400
6:49786356:CA:C	donor_gain	0.5900
6:49786353:TTA:T	donor_gain	0.5000
6:49786355:A:AC	donor_gain	0.5000
6:49786356:C:CC	donor_gain	0.5000
6:49786190:AG:A	donor_gain	0.4700
6:49786574:A:AC	donor_gain	0.4600
6:49786575:C:CC	donor_gain	0.4600
6:49786356:CACCA:C	donor_gain	0.4500
6:49786355:ACAC:A	donor_gain	0.4400
6:49786356:CACC:C	donor_gain	0.4400
6:49786570:T:TA	donor_gain	0.4200
6:49785977:T:A	donor_gain	0.4000
6:49785934:C:CT	donor_gain	0.3800
6:49785935:T:TT	donor_gain	0.3800
6:49786166:CCTA:C	donor_gain	0.3800
6:49786324:A:T	acceptor_gain	0.3800
6:49786403:C:CA	donor_gain	0.3800
6:49786475:C:CT	donor_gain	0.3700
6:49786348:AAT:A	donor_gain	0.3600
6:49786294:A:T	donor_gain	0.3500
6:49786607:AGTT:A	donor_gain	0.3500
6:49786290:TTCCA:T	donor_gain	0.3400
6:49786291:TCCA:T	donor_gain	0.3400
6:49786350:T:TA	donor_gain	0.3400
6:49786351:CCTTA:C	donor_loss	0.3300
6:49786352:CTTAC:C	donor_loss	0.3300
6:49786353:TTAC:T	donor_loss	0.3300

AlphaMissense

2758 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
6:49786676:C:G	R171P	1.000
6:49786009:G:C	S393R	0.999
6:49786009:G:T	S393R	0.999
6:49786011:T:G	S393R	0.999
6:49786677:G:T	R171S	0.999
6:49786690:A:C	F166L	0.999
6:49786690:A:T	F166L	0.999
6:49786692:A:G	F166L	0.999
6:49786825:G:C	N121K	0.999
6:49786825:G:T	N121K	0.999
6:49786999:A:C	H63Q	0.999
6:49786999:A:T	H63Q	0.999
6:49787001:G:C	H63D	0.999
6:49785991:A:C	S399R	0.998
6:49785991:A:T	S399R	0.998
6:49785993:T:G	S399R	0.998
6:49786004:C:T	G395E	0.998
6:49786159:A:C	F343L	0.998
6:49786159:A:T	F343L	0.998
6:49786161:A:G	F343L	0.998
6:49786528:C:A	K220N	0.998
6:49786528:C:G	K220N	0.998
6:49786529:T:A	K220M	0.998
6:49786530:T:C	K220E	0.998
6:49786530:T:G	K220Q	0.998
6:49786628:C:T	G187E	0.998
6:49786677:G:C	R171G	0.998
6:49786688:C:T	G167D	0.998
6:49786821:G:T	R123S	0.998
6:49787000:T:C	H63R	0.998

dbSNP variants (sampled 300 via entrez): RS1000360388 (6:49788907 A>G), RS1000412751 (6:49788647 C>T), RS1000695881 (6:49787552 C>T), RS1001409564 (6:49788694 G>T), RS1002371405 (6:49786593 T>C), RS1002706784 (6:49785186 T>A), RS1002737982 (6:49785446 T>G), RS1003453552 (6:49785438 CT>C,CTT), RS1004545661 (6:49787887 T>C), RS1004610861 (6:49789199 G>A,T), RS1005435847 (6:49787968 A>C,G), RS1005488205 (6:49787669 A>G), RS1006173253 (6:49786824 G>A), RS1006508471 (6:49785508 T>C), RS1007567630 (6:49789004 G>C)

Disease associations

OMIM: gene MIM:172270 | disease phenotypes:

GenCC curated gene-disease

Disease	Classification	Inheritance
male infertility with azoospermia or oligozoospermia due to single gene mutation	Moderate	Autosomal recessive

Mondo (1): (MONDO:0018393)

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL2096677 (PROTEIN FAMILY)

PharmGKB: 1 entry (VIP=true, CPIC=false)

ChEMBL bioactivities

26 potent at pChembl≥5 of 49 total, top 26 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChembl	Type	Value	Unit	Molecule
6.48	Ki	330	nM	CHEMBL348433
6.16	Ki	690	nM	CHEMBL356436
6.08	IC50	840	nM	CHEMBL150751
6.06	IC50	880	nM	CHEMBL151887
6.02	IC50	960	nM	CHEMBL150369
6.01	IC50	980	nM	CHEMBL357952
6.00	IC50	1000	nM	CHEMBL348186
6.00	IC50	1000	nM	CHEMBL356655
5.97	IC50	1080	nM	CHEMBL149734
5.94	IC50	1150	nM	CHEMBL149786
5.93	IC50	1170	nM	CHEMBL148974
5.89	IC50	1300	nM	CHEMBL356436
5.87	IC50	1340	nM	CHEMBL348433
5.75	IC50	1800	nM	CHEMBL422133
5.70	Kd	2000	nM	CHEMBL85343
5.70	IC50	1980	nM	CHEMBL347337
5.44	IC50	3600	nM	CHEMBL149264
5.40	Kd	4000	nM	CHEMBL85343
5.40	Kd	4000	nM	CHEMBL88020
5.22	Kd	6000	nM	CHEMBL1160562
5.16	Kd	7000	nM	CHEMBL85343
5.16	Kd	7000	nM	CHEMBL88020
5.10	Kd	8000	nM	CHEMBL88020
5.10	IC50	8000	nM	CHEMBL149115
5.08	IC50	8350	nM	CHEMBL149058
5.03	IC50	9400	nM	CHEMBL149129

PubChem BioAssay actives

20 with measured affinity, of 260 total; 18 most potent distinct compounds. Largely complementary to BindingDB; screening values are coarse (µM, 4 dp), so sub-nM hits tie at the floor.

Compound	Assay	Type	Value	Unit
[chloro-[6-[chloro(phosphono)methyl]-2-pyridinyl]methyl]phosphonic acid	3271: Binding affinity was evaluated towards 3-phosphoglycerate kinase at 37 degrees Celsius in 0.1 m NaCl pH 7.1	ki	0.3300	uM
[fluoro-[3-[fluoro(phosphono)methyl]phenyl]methyl]phosphonic acid	3271: Binding affinity was evaluated towards 3-phosphoglycerate kinase at 37 degrees Celsius in 0.1 m NaCl pH 7.1	ki	0.6900	uM
[[5-[difluoro(phosphono)methyl]-2,4-dimethylphenyl]-difluoromethyl]phosphonic acid	3270: Inhibitory activity against 3-phosphoglycerate kinase.	ic50	0.8400	uM
[[3-[difluoro(phosphono)methyl]-5-methylphenyl]-difluoromethyl]phosphonic acid	3270: Inhibitory activity against 3-phosphoglycerate kinase.	ic50	0.8800	uM
[[3-[difluoro(phosphono)methyl]phenyl]-difluoromethyl]phosphonic acid	3270: Inhibitory activity against 3-phosphoglycerate kinase.	ic50	0.9600	uM
[[4-[difluoro(phosphono)methyl]phenyl]-difluoromethyl]phosphonic acid	3270: Inhibitory activity against 3-phosphoglycerate kinase.	ic50	0.9800	uM
[3-[difluoro(phosphono)methyl]phenyl]phosphonic acid	3270: Inhibitory activity against 3-phosphoglycerate kinase.	ic50	1.0000	uM
[chloro-[3-[chloro(phosphono)methyl]phenyl]methyl]phosphonic acid	3270: Inhibitory activity against 3-phosphoglycerate kinase.	ic50	1.0000	uM
[chloro-[4-[chloro(phosphono)methyl]phenyl]methyl]phosphonic acid	3270: Inhibitory activity against 3-phosphoglycerate kinase.	ic50	1.0800	uM
[fluoro-[4-[fluoro(phosphono)methyl]phenyl]methyl]phosphonic acid	3270: Inhibitory activity against 3-phosphoglycerate kinase.	ic50	1.1500	uM
[[6-[difluoro(phosphono)methyl]-2-pyridinyl]-difluoromethyl]phosphonic acid	3270: Inhibitory activity against 3-phosphoglycerate kinase.	ic50	1.1700	uM
[3-[difluoro(phosphono)methyl]phenyl]methylphosphonic acid	3270: Inhibitory activity against 3-phosphoglycerate kinase.	ic50	1.8000	uM
[4-[difluoro(phosphono)methyl]phenyl]methylphosphonic acid	3270: Inhibitory activity against 3-phosphoglycerate kinase.	ic50	1.9800	uM
[dichloro-[3-[dichloro(phosphono)methyl]phenyl]methyl]phosphonic acid	3270: Inhibitory activity against 3-phosphoglycerate kinase.	ic50	3.6000	uM
[5-[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-hydroxyphosphoryl]-1,1,5,5-tetrafluoropentyl]phosphonic acid	158480: Dissociation constant for binding with Phosphoglycerate kinase (PGK) enzyme is evaluated	kd	6.0000	uM
[3-[chloro(phosphono)methyl]phenyl]methylphosphonic acid	3270: Inhibitory activity against 3-phosphoglycerate kinase.	ic50	8.0000	uM
[3-[fluoro(phosphono)methyl]phenyl]methylphosphonic acid	3270: Inhibitory activity against 3-phosphoglycerate kinase.	ic50	8.3500	uM
[4-[chloro(phosphono)methyl]phenyl]methylphosphonic acid	3270: Inhibitory activity against 3-phosphoglycerate kinase.	ic50	9.4000	uM

CTD chemical–gene interactions

10 total (human), top 10 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
bisphenol A	decreases methylation	1
sodium arsenite	affects expression	1
epigallocatechin gallate	decreases expression	1
bromovanin	decreases expression	1
bisphenol AF	increases expression	1
Amiodarone	increases expression	1
Benzo(a)pyrene	increases methylation, affects methylation	1
Caffeine	decreases expression	1
Graphite	decreases expression	1
Nanotubes, Carbon	decreases expression	1

ChEMBL screening assays

12 unique, capped per target: 12 binding

Representative assays (with source publication via chembl_document):

Assay ID	Type	Description	Source paper
CHEMBL615425	Binding	Binding affinity was evaluated towards 3-phosphoglycerate kinase at 37 degrees Celsius in 0.1 m NaCl pH 7.1	Novel bisphosphonate inhibitors of phosphoglycerate kinase. — Bioorg Med Chem Lett

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.