Showing Compound Card for Glyceric acid 1,3-biphosphate (CDB005086)

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IdentificationTaxonomyOntologyPhysical propertiesSpectraProtein targetPathwaysConcentrationsLinksReferencesenzymes (11) Show 11 proteinsXML
Record Information
Version1.0
Created at2020-04-17 19:07:55 UTC
Updated at2020-12-07 19:11:32 UTC
CannabisDB IDCDB005086
Secondary Accession NumbersNot Available
Cannabis Compound Identification
Common NameGlyceric acid 1,3-biphosphate
DescriptionGlyceric acid 1,3-biphosphate, also known as 1,3-bisphospho-D-glycerate or 3-phospho-D-glyceroyl phosphate, belongs to the class of organic compounds known as acyl monophosphates. These are organic compounds containing a monophosphate linked to an acyl group. They have the general structure R-CO-P(O)(O)OH, R=H or organyl. The (R)-enantiomer of 3-phosphoglyceroyl dihydrogen phosphate. Glyceric acid 1,3-biphosphate is an extremely weak basic (essentially neutral) compound (based on its pKa). Glyceric acid 1,3-biphosphate exists in all living species, ranging from bacteria to humans. Within humans, glyceric acid 1,3-biphosphate participates in a number of enzymatic reactions. In particular, glyceric acid 1,3-biphosphate can be biosynthesized from D-glyceraldehyde 3-phosphate; which is catalyzed by the enzyme glyceraldehyde-3-phosphate dehydrogenase. In addition, glyceric acid 1,3-biphosphate can be biosynthesized from 3-phosphoglyceric acid through the action of the enzyme pantothenate kinase 1. In humans, glyceric acid 1,3-biphosphate is involved in the metabolic disorder called the glycogen storage disease type 1A (gsd1a) or von gierke disease pathway. Outside of the human body, Glyceric acid 1,3-biphosphate has been detected, but not quantified in, several different foods, such as cherry tomato, jostaberries, canada blueberries, lovages, and mamey sapotes. This could make glyceric acid 1,3-biphosphate a potential biomarker for the consumption of these foods. Glyceric acid 1,3-biphosphate is expected to be in Cannabis as all living plants are known to produce and metabolize it.
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
ValueSource
(R)-2-Hydroxy-3-(phosphonooxy)-1-monoanhydride with phosphoric propanoic acidChEBI
1,3-Bisphospho-D-glycerateChEBI
3-Phospho-D-glyceroyl phosphateChEBI
D-Glycerate 1,3-diphosphateKegg
(R)-2-Hydroxy-3-(phosphonooxy)-1-monoanhydride with phosphoric propanoateGenerator
1,3-Bisphospho-D-glyceric acidGenerator
3-Phospho-D-glyceroyl phosphoric acidGenerator
D-Glyceric acid 1,3-diphosphoric acidGenerator
Glycerate 1,3-biphosphateGenerator
Glyceric acid 1,3-biphosphoric acidGenerator
3-Phospho-D-glyceroyl dihydrogen phosphoric acidHMDB
1,3-BiphosphoglycerateHMDB
1,3-BisphosphoglycerateHMDB
1,3-Bisphosphoglyceric acidHMDB
1,3-DiphosphoglycerateHMDB
1,3-Diphosphoglyceric acidHMDB
3-Phospho-D-glyceroyl-phosphateHMDB
3-Phosphoglyceroyl phosphateHMDB
3-Phosphoglyceroyl-pHMDB
3-Phosphoglyceroyl-phosphateHMDB
3-Phosphonato-D-glyceroyl phosphateHMDB
3-Phosphonatoglyceroyl phosphateHMDB
3-p-Glyceroyl-pHMDB
D-Glycerate 1,3-biphosphateHMDB
D-Glycerate 1,3-bisphosphateHMDB
D-Glyceric acid 1,3-biphosphateHMDB
D-Glyceric acid 1,3-bisphosphateHMDB
D-Glyceric acid 1,3-diphosphateHMDB
DPGHMDB
Glycerate 1,3-bisphosphateHMDB
Glycerate 1,3-diphosphateHMDB
Glyceric acid 1,3-bisphosphateHMDB
Glyceric acid 1,3-diphosphateHMDB
Phosphoglyceroyl-pHMDB
p-Glyceroyl-pHMDB
Glyceric acid 1,3-biphosphateHMDB
Chemical FormulaC3H8O10P2
Average Molecular Weight266.04
Monoisotopic Molecular Weight265.9593
IUPAC Name{[(2R)-2-hydroxy-3-(phosphonooxy)propanoyl]oxy}phosphonic acid
Traditional Name1,3-bisphospho-D-glycerate
CAS Registry Number38168-82-0
SMILES
O[C@H](COP(O)(O)=O)C(=O)OP(O)(O)=O
InChI Identifier
InChI=1S/C3H8O10P2/c4-2(1-12-14(6,7)8)3(5)13-15(9,10)11/h2,4H,1H2,(H2,6,7,8)(H2,9,10,11)/t2-/m1/s1
InChI KeyLJQLQCAXBUHEAZ-UWTATZPHSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as acyl monophosphates. These are organic compounds containing a monophosphate linked to an acyl group. They have the general structure R-CO-P(O)(O)OH, R=H or organyl.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassOrganic phosphoric acids and derivatives
Sub ClassPhosphate esters
Direct ParentAcyl monophosphates
Alternative Parents
Substituents
  • Acyl monophosphate
  • Glyceric_acid
  • Monoalkyl phosphate
  • Monosaccharide
  • Alkyl phosphate
  • Carboxylic acid salt
  • Secondary alcohol
  • Monocarboxylic acid or derivatives
  • Carboxylic acid derivative
  • Organic oxide
  • Organooxygen compound
  • Organic oxygen compound
  • Alcohol
  • Carbonyl group
  • Hydrocarbon derivative
  • Organic salt
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Physiological effect

Health effect:

Disposition

Source:

Biological location:

Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
logPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP-1.1ALOGPS
logP-2.3ChemAxon
logS-1.4ALOGPS
pKa (Strongest Acidic)1.01ChemAxon
pKa (Strongest Basic)-4.2ChemAxon
Physiological Charge-4ChemAxon
Hydrogen Acceptor Count8ChemAxon
Hydrogen Donor Count5ChemAxon
Polar Surface Area170.82 ŲChemAxon
Rotatable Bond Count6ChemAxon
Refractivity42.42 m³·mol⁻¹ChemAxon
Polarizability18.01 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Spectra
EI-MS/GC-MS
TypeDescriptionSplash KeyView
Predicted GC-MSGlyceric acid 1,3-biphosphate, non-derivatized, Predicted GC-MS Spectrum - 70eV, Positivesplash10-0002-9500000000-cb3071f9249ee92b7d2cSpectrum
Predicted GC-MSGlyceric acid 1,3-biphosphate, non-derivatized, Predicted GC-MS Spectrum - 70eV, PositiveNot AvailableSpectrum
MS/MS
TypeDescriptionSplash KeyView
Predicted MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-014i-1950000000-2cde7b5739871a8825422015-09-15View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-014m-3910000000-72f2c46eab20369380562015-09-15View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-000f-9500000000-c835034f0ac11618922d2015-09-15View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-03fr-6190000000-6f4870543fc6131d14a72015-09-15View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004i-9000000000-d9d9c6d217a255d791fd2015-09-15View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9000000000-1fef400a1ea8ca54c8022015-09-15View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-03dj-0090000000-def40aa9bb3094302ce82021-09-22View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-01r2-9040000000-374a9ff8c866f10f2f3c2021-09-22View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9000000000-4bf2b9a14f4e1c8fc62a2021-09-22View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-00kb-1390000000-8fe62bbfc56bf59f28a62021-09-22View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0002-9410000000-e17767e21640a6f815322021-09-22View Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0002-9000000000-c41dab2684b9d54afd312021-09-22View Spectrum
NMRNot Available
Pathways
Pathways
Protein Targets
Enzymes
Protein NameGene NameLocusUniprot IDDetails
Bisphosphoglycerate mutaseBPGM7q33P07738 details
Phosphoglycerate mutase 2PGAM27p13-p12P15259 details
Probable phosphoglycerate mutase 4PGAM4Xq13Q8N0Y7 details
Phosphoglycerate mutase 1PGAM110q25.3P18669 details
Acylphosphatase-2ACYP22p16.2P14621 details
Acylphosphatase-1ACYP114q24.3P07311 details
Glyceraldehyde-3-phosphate dehydrogenase, testis-specificGAPDHS19q13.12O14556 details
Glyceraldehyde-3-phosphate dehydrogenaseGAPDH12p13P04406 details
Phosphoglycerate kinase 2PGK26p12.3P07205 details
Phosphoglycerate kinase 1PGK1Xq13.3P00558 details
Glucose 1,6-bisphosphate synthasePGM2L111q13.4Q6PCE3 details
TransportersNot Available
Metal BindingsNot Available
ReceptorsNot Available
Transcriptional FactorsNot Available
Concentrations Data
Not Available
HMDB IDHMDB0001270
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB030188
KNApSAcK IDC00019552
Chemspider IDNot Available
KEGG Compound IDC00236
BioCyc IDDPG
BiGG IDNot Available
Wikipedia Link1,3-Bisphosphoglyceric acid
METLIN IDNot Available
PubChem Compound439191
PDB IDNot Available
ChEBI ID16001
References
General ReferencesNot Available

Only showing the first 10 proteins. There are 11 proteins in total.

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Enzymes

Enzyme Details
1. Bisphosphoglycerate mutase
General function:
Involved in catalytic activity
Specific function:
Plays a major role in regulating hemoglobin oxygen affinity by controlling the levels of its allosteric effector 2,3-bisphosphoglycerate (2,3-BPG). Also exhibits mutase (EC 5.4.2.1) and phosphatase (EC 3.1.3.13) activities.
Gene Name:
BPGM
Uniprot ID:
P07738
Molecular weight:
30004.98
Enzyme Details
2. Phosphoglycerate mutase 2
General function:
Involved in catalytic activity
Specific function:
Interconversion of 3- and 2-phosphoglycerate with 2,3-bisphosphoglycerate as the primer of the reaction. Can also catalyze the reaction of EC 5.4.2.4 (synthase) and EC 3.1.3.13 (phosphatase), but with a reduced activity.
Gene Name:
PGAM2
Uniprot ID:
P15259
Molecular weight:
28765.96
Enzyme Details
3. Probable phosphoglycerate mutase 4
General function:
Involved in catalytic activity
Specific function:
Not Available
Gene Name:
PGAM4
Uniprot ID:
Q8N0Y7
Molecular weight:
28776.605
Enzyme Details
4. Phosphoglycerate mutase 1
General function:
Involved in catalytic activity
Specific function:
Interconversion of 3- and 2-phosphoglycerate with 2,3-bisphosphoglycerate as the primer of the reaction. Can also catalyze the reaction of EC 5.4.2.4 (synthase) and EC 3.1.3.13 (phosphatase), but with a reduced activity.
Gene Name:
PGAM1
Uniprot ID:
P18669
Molecular weight:
28803.675
Enzyme Details
5. Acylphosphatase-2
General function:
Involved in acylphosphatase activity
Specific function:
Its physiological role is not yet clear.
Gene Name:
ACYP2
Uniprot ID:
P14621
Molecular weight:
11139.52
Enzyme Details
6. Acylphosphatase-1
General function:
Involved in acylphosphatase activity
Specific function:
Its physiological role is not yet clear.
Gene Name:
ACYP1
Uniprot ID:
P07311
Molecular weight:
11260.84
Enzyme Details
7. Glyceraldehyde-3-phosphate dehydrogenase, testis-specific
General function:
Involved in glyceraldehyde-3-phosphate dehydrogenase activity
Specific function:
May play an important role in regulating the switch between different pathways for energy production during spermiogenesis and in the spermatozoon. Required for sperm motility and male fertility (By similarity).
Gene Name:
GAPDHS
Uniprot ID:
O14556
Molecular weight:
44500.835
Enzyme Details
8. Glyceraldehyde-3-phosphate dehydrogenase
General function:
Involved in glyceraldehyde-3-phosphate dehydrogenase activity
Specific function:
Has both glyceraldehyde-3-phosphate dehydrogenase and nitrosylase activities, thereby playing a role in glycolysis and nuclear functions, respectively. Participates in nuclear events including transcription, RNA transport, DNA replication and apoptosis. Nuclear functions are probably due to the nitrosylase activity that mediates cysteine S-nitrosylation of nuclear target proteins such as SIRT1, HDAC2 and PRKDC. Modulates the organization and assembly of the cytoskeleton. Facilitates the CHP1-dependent microtubule and membrane associations through its ability to stimulate the binding of CHP1 to microtubules (By similarity). Glyceraldehyde-3-phosphate dehydrogenase is a key enzyme in glycolysis that catalyzes the first step of the pathway by converting D-glyceraldehyde 3-phosphate (G3P) into 3-phospho-D-glyceroyl phosphate. Component of the GAIT (gamma interferon-activated inhibitor of translation) complex which mediates interferon-gamma-induced transcript-selective translation inhibition in inflammation processes. Upon interferon-gamma treatment assembles into the GAIT complex which binds to stem loop-containing GAIT elements in the 3'-UTR of diverse inflammatory mRNAs (such as ceruplasmin) and suppresses their translation.
Gene Name:
GAPDH
Uniprot ID:
P04406
Molecular weight:
31547.76
Enzyme Details
9. Phosphoglycerate kinase 2
General function:
Carbohydrate transport and metabolism
Specific function:
Not Available
Gene Name:
PGK2
Uniprot ID:
P07205
Molecular weight:
44795.79
Enzyme Details
10. Phosphoglycerate kinase 1
General function:
Involved in phosphoglycerate kinase activity
Specific function:
In addition to its role as a glycolytic enzyme, it seems that PGK-1 acts as a polymerase alpha cofactor protein (primer recognition protein).
Gene Name:
PGK1
Uniprot ID:
P00558
Molecular weight:
44614.36

Only showing the first 10 proteins. There are 11 proteins in total.

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