MiMeDB: Showing metabocard for 6-Phosphonoglucono-D-lactone (MMDBc0029565)

Plant

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-17 23:32:30 UTC

Update Date

2022-08-31 13:43:52 UTC

Metabolite ID

MMDBc0029565

Metabolite Identification

Common Name

6-Phosphonoglucono-D-lactone

Description

6-phosphoglucono-delta-lactone (d-6PGL) is the immediate product of the Glucose-6-phosphate dehydrogenase (G-6-PD), the first enzyme of the hexose monophosphate pathway. (PMID 3711719 )

Structure

MOL 3D MOL SDF 3D SDF PDB 3D PDB SMILES InChI


  Mrv1652309042000182D          

 16 16  0  0  1  0            999 V2000
   -2.0366    0.3892    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2129    0.3892    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8566    0.3892    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0366    1.2129    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0366   -0.4308    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5025    0.8010    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2116    0.3892    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.2116   -0.4420    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.9220    0.8010    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9220   -0.8615    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.5025   -0.8502    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6437    0.3892    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6437   -0.4420    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.9220   -1.6852    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3541    0.8010    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3541   -0.8502    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  1  0  0  0  0
  1  4  1  0  0  0  0
  1  5  2  0  0  0  0
  2  6  1  0  0  0  0
  7  6  1  1  0  0  0
  7  8  1  0  0  0  0
  7  9  1  0  0  0  0
  8 10  1  0  0  0  0
  8 11  1  6  0  0  0
  9 12  1  0  0  0  0
 10 13  1  0  0  0  0
 10 14  1  1  0  0  0
 12 15  2  0  0  0  0
 13 16  1  6  0  0  0
 12 13  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0029565

> <DATABASE_NAME>
MIME

> <SMILES>
O[C@H]1[C@H](O)[C@@H](COP(O)(O)=O)OC(=O)[C@@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C6H11O9P/c7-3-2(1-14-16(11,12)13)15-6(10)5(9)4(3)8/h2-5,7-9H,1H2,(H2,11,12,13)/t2-,3-,4+,5-/m1/s1

> <INCHI_KEY>
IJOJIVNDFQSGAB-SQOUGZDYSA-N

> <FORMULA>
C6H11O9P

> <MOLECULAR_WEIGHT>
258.1199

> <EXACT_MASS>
258.014068462

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
27

> <JCHEM_AVERAGE_POLARIZABILITY>
19.902164898548747

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
{[(2R,3S,4S,5R)-3,4,5-trihydroxy-6-oxooxan-2-yl]methoxy}phosphonic acid

> <ALOGPS_LOGP>
-1.99

> <JCHEM_LOGP>
-2.8688392173333335

> <ALOGPS_LOGS>
-0.90

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
6.329575480706394

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.3037364832915905

> <JCHEM_PKA_STRONGEST_BASIC>
-3.6629249867193456

> <JCHEM_POLAR_SURFACE_AREA>
153.75

> <JCHEM_REFRACTIVITY>
45.651700000000005

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.26e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
6-phosphogluconolactone

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 04-SEP-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-SEP-20         0                                  
HETATM    1  P   UNK     0      -3.802   0.727   0.000  0.00  0.00           P+0
HETATM    2  O   UNK     0      -2.264   0.727   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0      -5.332   0.727   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0      -3.802   2.264   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0      -3.802  -0.804   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0      -0.938   1.495   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.395   0.727   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.395  -0.825   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       1.721   1.495   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0       1.721  -1.608   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0      -0.938  -1.587   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0       3.068   0.727   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       3.068  -0.825   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0       1.721  -3.146   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0       4.394   1.495   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0       4.394  -1.587   0.000  0.00  0.00           O+0
CONECT    1    2    3    4    5                                             
CONECT    2    1    6                                                       
CONECT    3    1                                                            
CONECT    4    1                                                            
CONECT    5    1                                                            
CONECT    6    2    7                                                       
CONECT    7    6    8    9                                                  
CONECT    8    7   10   11                                                  
CONECT    9    7   12                                                       
CONECT   10    8   13   14                                                  
CONECT   11    8                                                            
CONECT   12    9   15   13                                                  
CONECT   13   10   16   12                                                  
CONECT   14   10                                                            
CONECT   15   12                                                            
CONECT   16   13                                                            
MASTER        0    0    0    0    0    0    0    0   16    0   32    0
END

COMPND    HMDB0001127
HETATM    1  O1  UNL     1      -2.517  -1.462  -2.297  1.00  0.00           O  
HETATM    2  C1  UNL     1      -1.892  -0.972  -1.321  1.00  0.00           C  
HETATM    3  O2  UNL     1      -0.531  -0.653  -1.377  1.00  0.00           O  
HETATM    4  C2  UNL     1      -0.038   0.515  -0.754  1.00  0.00           C  
HETATM    5  C3  UNL     1       1.460   0.386  -0.670  1.00  0.00           C  
HETATM    6  O3  UNL     1       1.858  -0.725   0.068  1.00  0.00           O  
HETATM    7  P1  UNL     1       3.552  -0.733   0.071  1.00  0.00           P  
HETATM    8  O4  UNL     1       4.097  -0.706  -1.359  1.00  0.00           O  
HETATM    9  O5  UNL     1       4.179   0.615   0.861  1.00  0.00           O  
HETATM   10  O6  UNL     1       4.147  -2.127   0.818  1.00  0.00           O  
HETATM   11  C4  UNL     1      -0.681   0.791   0.562  1.00  0.00           C  
HETATM   12  O7  UNL     1      -0.393   2.117   0.930  1.00  0.00           O  
HETATM   13  C5  UNL     1      -2.184   0.709   0.391  1.00  0.00           C  
HETATM   14  O8  UNL     1      -2.868   1.128   1.530  1.00  0.00           O  
HETATM   15  C6  UNL     1      -2.573  -0.695  -0.020  1.00  0.00           C  
HETATM   16  O9  UNL     1      -3.955  -0.750  -0.209  1.00  0.00           O  
HETATM   17  H1  UNL     1      -0.257   1.368  -1.428  1.00  0.00           H  
HETATM   18  H2  UNL     1       1.953   1.283  -0.257  1.00  0.00           H  
HETATM   19  H3  UNL     1       1.864   0.246  -1.693  1.00  0.00           H  
HETATM   20  H4  UNL     1       5.012   0.956   0.428  1.00  0.00           H  
HETATM   21  H5  UNL     1       3.437  -2.821   0.793  1.00  0.00           H  
HETATM   22  H6  UNL     1      -0.374   0.083   1.360  1.00  0.00           H  
HETATM   23  H7  UNL     1      -1.060   2.708   0.493  1.00  0.00           H  
HETATM   24  H8  UNL     1      -2.473   1.382  -0.457  1.00  0.00           H  
HETATM   25  H9  UNL     1      -3.429   0.352   1.835  1.00  0.00           H  
HETATM   26  H10 UNL     1      -2.215  -1.424   0.735  1.00  0.00           H  
HETATM   27  H11 UNL     1      -4.118  -1.568  -0.756  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3   15
CONECT    3    4
CONECT    4    5   11   17
CONECT    5    6   18   19
CONECT    6    7
CONECT    7    8    8    9   10
CONECT    9   20
CONECT   10   21
CONECT   11   12   13   22
CONECT   12   23
CONECT   13   14   15   24
CONECT   14   25
CONECT   15   16   26
CONECT   16   27
END

Synonyms

Value	Source
6-Phospho-D-glucono-1,5-lactone	ChEBI
6-Phosphonoglucono-delta-lactone	ChEBI
[(2R,3S,4S,5R)-3,4,5-Trihydroxy-6-oxotetrahydro-2H-pyran-2-yl]methyl dihydrogen phosphate	ChEBI
D-Gluconic acid, delta-lactone, 6-(dihydrogen phosphate)	ChEBI
D-Glucono-1,5-lactone 6-phosphate	ChEBI
6-Phosphonoglucono-δ-lactone	Generator
[(2R,3S,4S,5R)-3,4,5-Trihydroxy-6-oxotetrahydro-2H-pyran-2-yl]methyl dihydrogen phosphoric acid	Generator
D-Gluconate, delta-lactone, 6-(dihydrogen phosphate)	Generator
D-Gluconate, δ-lactone, 6-(dihydrogen phosphate)	Generator
D-Gluconic acid, delta-lactone, 6-(dihydrogen phosphoric acid)	Generator
D-Gluconic acid, δ-lactone, 6-(dihydrogen phosphoric acid)	Generator
D-Glucono-1,5-lactone 6-phosphoric acid	Generator
6-(Dihydrogen phosphate)-(8ci)-D-gluconic acid delta-lactone	HMDB
6-(Dihydrogen phosphate)-(9ci)-D-gluconic acid delta-lactone	HMDB
6-(Dihydrogen phosphate)-D-gluconic acid delta-lactone	HMDB
6-PGDL	HMDB
6-Phosphoglucono-delta-lactone	HMDB
6-Phosphogluconolactone	HMDB
D-6-Phospho-glucono-delta-lactone	HMDB
D-6-Phosphoglucono-delta-lactone	HMDB
D-Glucono-delta-lactone-6-phosphate	HMDB
delta-Gluconolactone 6-phosphate	HMDB
p-Gluconolactone	HMDB

Molecular Formula

C₆H₁₁O₉P

Average Mass

258.1199

Monoisotopic Mass

258.014068462

IUPAC Name

{[(2R,3S,4S,5R)-3,4,5-trihydroxy-6-oxooxan-2-yl]methoxy}phosphonic acid

Traditional Name

6-phosphogluconolactone

CAS Registry Number

2641-81-8

SMILES

O[C@H]1[C@H](O)[C@@H](COP(O)(O)=O)OC(=O)[C@@H]1O

InChI Identifier

InChI=1S/C6H11O9P/c7-3-2(1-14-16(11,12)13)15-6(10)5(9)4(3)8/h2-5,7-9H,1H2,(H2,11,12,13)/t2-,3-,4+,5-/m1/s1

InChI Key

IJOJIVNDFQSGAB-SQOUGZDYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as hexose phosphates. These are carbohydrate derivatives containing a hexose substituted by one or more phosphate groups.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Hexose phosphates

Alternative Parents

Substituents

Hexose phosphate
Gluconolactone
Monosaccharide phosphate
Delta valerolactone
Delta_valerolactone
Monoalkyl phosphate
Alkyl phosphate
Organic phosphoric acid derivative
Phosphoric acid ester
Oxane
Secondary alcohol
Carboxylic acid ester
Lactone
Organoheterocyclic compound
Carboxylic acid derivative
Monocarboxylic acid or derivatives
Oxacycle
Polyol
Hydrocarbon derivative
Organic oxide
Alcohol
Carbonyl group
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

aldonolactone phosphate (CHEBI:16938 )

Functional Ontology

Not Available

Physical Properties

State

Solid

Predicted Properties

Property	Value	Source
Water Solubility	32.6 g/L	ALOGPS
logP	-2	ALOGPS
logP	-2.9	ChemAxon
logS	-0.9	ALOGPS
pKa (Strongest Acidic)	1.3	ChemAxon
pKa (Strongest Basic)	-3.7	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	153.75 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	45.65 m³·mol⁻¹	ChemAxon
Polarizability	19.9 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Chromatographic Retention Times and Retention Indices

Retention Times

Not Available

Retention Indices

Not Available

Chromatographic Retention Times and Retention Indices

Retention Times

Not Available

Retention Indices

Not Available

Biological Properties

Cellular Locations

Endoplasmic reticulum

Biospecimen Locations

Cellular Cytoplasm
Feces

Tissue Locations

Not Available

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Protein ID	Protein Name	Protein Type	Uniprot ID	Species
MMDBp0191996	6-phosphogluconolactonase	Enzyme	O95336	Homo_sapiens
MMDBp0191997	Glucose-6-phosphate 1-dehydrogenase	Enzyme	P11413	Homo_sapiens
MMDBp0191998	GDH/6PGL endoplasmic bifunctional protein	Unknown	O95479	Homo_sapiens

Human Pathways

Pathways

Name	SMPDB/PathBank

Microbial Pathways

Pathways

Not Available

Metabolic Reactions

Reactions

This table shows at most 20 reactions. For the full list of associated reactions:

See All Associated Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Evidence Type	Host and Biospecimen	Data Source	Reference

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
Bacteria	Proteobacteria	201	Pig ; Human feces; Human ; Human pleural fluid plaque; Human dental plaque; Human nasal swab; Human feces; pleural fluid plaque; bal	Unknown; Metabolic reconstruction
Bacteria	Firmicutes	253	Human feces; Human ; Pig ; Cattle	Metabolic reconstruction
Bacteria	Actinobacteria	107	Human feces; Human pleural fluid plaque; Human dental plaque; Human sputum; Human ; Cattle	Metabolic reconstruction
Bacteria	Bacteroidetes	79	Human feces; Human	Metabolic reconstruction
Bacteria	Fusobacteria	2	Human feces	Metabolic reconstruction
Bacteria	Planctomycetes	1	Human feces	Metabolic reconstruction
Eukaryota/Fungi	Ascomycota	11	Human feces	Unknown
Bacteria	Spirochaetes	2	Human
Bacteria	Chlamydiae	3	Human
Bacteria	Cyanobacteria	3
Bacteria	nah	1
Bacteria	Thermotogae	1
Bacteria/NULL	Bacteroidetes	1	Human feces; Human	Metabolic reconstruction
Eukaryota/Fungi	Microsporidia	1
Archaea/Archaea	Euryarchaeota	1

Exposure Sources

Food Exposures

Other Exposures

Source Type	Data Source	Reference

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference
Human Feces	Detected but not Quantified									HMDB
Human	Detected and Quantified	0.00762					Adult (>18 years old)	Both	Normal	HMDB	15882454

External Links

HMDB ID

HMDB0001127

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB030612

KNApSAcK ID

Not Available

Chemspider ID

388559

KEGG Compound ID

C01236

BioCyc ID

D-6-P-GLUCONO-DELTA-LACTONE

BiGG ID

37157

Wikipedia Link

Not Available

METLIN ID

6022

PubChem Compound

439452

PDB ID

Not Available

ChEBI ID

16938

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

Not Available

General References

Beutler E, Kuhl W: Characteristics and significance of the reverse glucose-6-phosphate dehydrogenase reaction. J Lab Clin Med. 1986 Jun;107(6):502-7. [PubMed:3711719 ]
Rakitzis ET, Papandreou P: Kinetic analysis of 6-phosphogluconolactone hydrolysis in hemolysates. Biochem Mol Biol Int. 1995 Nov;37(4):747-55. [PubMed:8589648 ]
Miclet E, Stoven V, Michels PA, Opperdoes FR, Lallemand JY, Duffieux F: NMR spectroscopic analysis of the first two steps of the pentose-phosphate pathway elucidates the role of 6-phosphogluconolactonase. J Biol Chem. 2001 Sep 14;276(37):34840-6. doi: 10.1074/jbc.M105174200. Epub 2001 Jul 16. [PubMed:11457850 ]
Nakayama Y, Kinoshita A, Tomita M: Dynamic simulation of red blood cell metabolism and its application to the analysis of a pathological condition. Theor Biol Med Model. 2005 May 9;2:18. doi: 10.1186/1742-4682-2-18. [PubMed:15882454 ]

Showing metabocard for 6-Phosphonoglucono-D-lactone (MMDBc0029565)

MOL for #<Metabolite:0x00007f12410cac88>

3D MOL for #<Metabolite:0x00007f12410cac88>

3D SDF for #<Metabolite:0x00007f12410cac88>

3D-SDF for #<Metabolite:0x00007f12410cac88>

PDB for #<Metabolite:0x00007f12410cac88>

3D PDB for #<Metabolite:0x00007f12410cac88>

SMILES for #<Metabolite:0x00007f12410cac88>

INCHI for #<Metabolite:0x00007f12410cac88>

Structure for #<Metabolite:0x00007f12410cac88>

3D Structure for #<Metabolite:0x00007f12410cac88>