MiMeDB: Showing metabocard for D-Glycero-D-manno-heptose 1-phosphate (MMDBc0031604)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-18 01:41:06 UTC

Update Date

2022-08-31 18:22:25 UTC

MiMeDB ID

MMDBc0031604

Metabolite Identification

Common Name

D-Glycero-D-manno-heptose 1-phosphate

Description

D-glycero-D-manno-heptose 1-phosphate is a member of the chemical class known as Hexoses. These are monosaccharides in which the sugar unit is a hexose. D-Glycero-D-manno-heptose 1-phosphate is involved in the biosynthesis of the lipopolysaccharide core precursor ADP-L-glycero-D-manno-heptose. (PMID 10629197 )

Structure

MOL SDF PDB SMILES InChI


  Mrv0541 07301213342D          

 24 24  0  0  0  0            999 V2000
   -0.7145    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    1.2375    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.4289   -0.0000    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -2.0625    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    1.0164   -2.3645    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    1.8414   -0.9355    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -1.6500    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1842    1.8695    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1468    1.6002    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2448    1.8695    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    0.4125    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2822    1.6002    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.8250    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  4  3  1  0  0  0  0
  5  3  1  0  0  0  0
  6  2  1  6  0  0  0
  6  4  1  0  0  0  0
  7  5  1  0  0  0  0
  8  1  1  0  0  0  0
  2  9  1  1  0  0  0
  3 10  1  6  0  0  0
  4 11  1  1  0  0  0
  5 12  1  6  0  0  0
 16  6  1  0  0  0  0
 16  7  1  0  0  0  0
 17  7  1  0  0  0  0
 18 13  1  0  0  0  0
 18 14  1  0  0  0  0
 18 15  2  0  0  0  0
 18 17  1  0  0  0  0
  2 19  1  1  0  0  0
  3 20  1  1  0  0  0
  4 21  1  6  0  0  0
  5 22  1  1  0  0  0
  6 23  1  1  0  0  0
 24  7  1  0  0  0  0
M  CHG  2  13  -1  14  -1
M  END
> <DATABASE_ID>
MMDBc0031604

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@@](O)(CO)[C@@]1([H])OC([H])(OP([O-])([O-])=O)[C@@]([H])(O)[C@@]([H])(O)[C@]1([H])O

> <INCHI_IDENTIFIER>
InChI=1S/C7H15O10P/c8-1-2(9)6-4(11)3(10)5(12)7(16-6)17-18(13,14)15/h2-12H,1H2,(H2,13,14,15)/p-2/t2-,3+,4+,5+,6-,7?/m1/s1

> <INCHI_KEY>
KMEJCSKJXSBBAN-NNPWBXLPSA-L

> <FORMULA>
C7H13O10P

> <MOLECULAR_WEIGHT>
288.1459

> <EXACT_MASS>
288.024633148

> <JCHEM_ACCEPTOR_COUNT>
9

> <JCHEM_AVERAGE_POLARIZABILITY>
22.964599319015214

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
-2

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3S,4S,5S,6R)-6-[(1R)-1,2-dihydroxyethyl]-3,4,5-trihydroxyoxan-2-yl phosphate

> <ALOGPS_LOGP>
-2.27

> <JCHEM_LOGP>
-3.6864401913333325

> <ALOGPS_LOGS>
-0.56

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
6.218846063852295

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.1553241541122095

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9745062434812723

> <JCHEM_POLAR_SURFACE_AREA>
182.79999999999998

> <JCHEM_REFRACTIVITY>
50.5154

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
8.97e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(3S,4S,5S,6R)-6-[(1R)-1,2-dihydroxyethyl]-3,4,5-trihydroxyoxan-2-yl phosphate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 30-JUL-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   30-JUL-12         0                                  
HETATM    1  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O-1
HETATM   14  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O-1
HETATM   15  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   18  P   UNK     0       0.000   0.000   0.000  0.00  0.00           P+0
HETATM   19  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   20  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   21  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   22  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   23  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   24  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
CONECT    1    2    8                                                       
CONECT    2    1    6    9   19                                             
CONECT    3    4    5   10   20                                             
CONECT    4    3    6   11   21                                             
CONECT    5    3    7   12   22                                             
CONECT    6    2    4   16   23                                             
CONECT    7    5   16   17   24                                             
CONECT    8    1                                                            
CONECT    9    2                                                            
CONECT   10    3                                                            
CONECT   11    4                                                            
CONECT   12    5                                                            
CONECT   13   18                                                            
CONECT   14   18                                                            
CONECT   15   18                                                            
CONECT   16    6    7                                                       
CONECT   17    7   18                                                       
CONECT   18   13   14   15   17                                             
CONECT   19    2                                                            
CONECT   20    3                                                            
CONECT   21    4                                                            
CONECT   22    5                                                            
CONECT   23    6                                                            
CONECT   24    7                                                            
MASTER        0    0    0    0    0    0    0    0   24    0   48    0
END

Synonyms

Value	Source
D-Glycero-D-manno-heptose 1-phosphoric acid	Generator

Chemical Formula

C₇H₁₃O₁₀P

Average Molecular Weight

288.1459

Monoisotopic Molecular Weight

288.024633148

IUPAC Name

(3S,4S,5S,6R)-6-[(1R)-1,2-dihydroxyethyl]-3,4,5-trihydroxyoxan-2-yl phosphate

Traditional Name

(3S,4S,5S,6R)-6-[(1R)-1,2-dihydroxyethyl]-3,4,5-trihydroxyoxan-2-yl phosphate

CAS Registry Number

Not Available

SMILES

[H][C@@](O)(CO)[C@@]1([H])OC([H])(OP([O-])([O-])=O)[C@@]([H])(O)[C@@]([H])(O)[C@]1([H])O

InChI Identifier

InChI=1S/C7H15O10P/c8-1-2(9)6-4(11)3(10)5(12)7(16-6)17-18(13,14)15/h2-12H,1H2,(H2,13,14,15)/p-2/t2-,3+,4+,5+,6-,7?/m1/s1

InChI Key

KMEJCSKJXSBBAN-NNPWBXLPSA-L

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as monosaccharide phosphates. These are monosaccharides comprising a phosphated group linked to the carbohydrate unit.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Monosaccharide phosphates

Alternative Parents

Substituents

Monosaccharide phosphate
Alkyl phosphate
Phosphoric acid ester
Oxane
Organic phosphoric acid derivative
Secondary alcohol
Oxacycle
Organoheterocyclic compound
Polyol
Organic oxide
Hydrocarbon derivative
Primary alcohol
Alcohol
Organic anion
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

aldoheptose phosphate (CHEBI:60002 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	89.7 g/L	ALOGPS
logP	-2.3	ALOGPS
logP	-3.7	ChemAxon
logS	-0.56	ALOGPS
pKa (Strongest Acidic)	1.16	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	9	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	182.8 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	50.52 m³·mol⁻¹	ChemAxon
Polarizability	22.96 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

Spectrum Type	Description	Splash Key	Deposition Date	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-000i-1290000000-aaa95c90e2c25ab1eb7a	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0bvi-5390000000-c7c93f6013718fe9653f	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-08or-9300000000-fd0ccf7f1c5b0851e0af	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-000i-5490000000-8f63d602921aa5a4ad22	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-06y9-9240000000-6456aee3da9be9939619	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0bt9-9200000000-e9fe10c075b6dd73eedb	2015-09-15	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, H₂O, predicted)		Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)		Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)		Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)		Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)		Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)		Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)		Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)		Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)		Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)		Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)		Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)		Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)		Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)		Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)		Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)		Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)		Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)		Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Feces

Tissue Locations

Not Available

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Proteins

Human Pathways

Pathways

Name	SMPDB/PathBank

Metabolic Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Related Health Condition	Evidence Type	Measured in Matrix	Data Source	Reference

Microbial Sources

Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
	Proteobacteria	172	Human Feces; Human ; Pig	Unknown; Metabolic reconstruction
	Firmicutes	71	Pig ; Human Feces; Human	Metabolic reconstruction
	Actinobacteria	89	Human Feces; Human	Metabolic reconstruction
	Verrucomicrobia	1	Human	Metabolic reconstruction
	Bacteroidetes	99	Human Feces; Human	Metabolic reconstruction
	Synergistetes	3	Human Feces	Metabolic reconstruction
	Spirochaetes	1	Human Feces	Metabolic reconstruction
	Thaumarchaeota	1	Human Feces	Metabolic reconstruction
	Fusobacteria	19	Human Feces; Human	Metabolic reconstruction
	Euryarchaeota	4	Human Feces; Cattle ; Human	Metabolic reconstruction
	Planctomycetes	1	Human Feces	Metabolic reconstruction
	Crenarchaeota	1	Human Feces	Metabolic reconstruction
	Chlorobi	1
Archaea	Euryarchaeota	2
	Cyanobacteria	1

Exposure Sources

Source Type	Source Sub-type	Species	Data Source	Reference	Details

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		details

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

46878581

PDB ID

Not Available

ChEBI ID

60002

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Noronha A, Modamio J, Jarosz Y, Guerard E, Sompairac N, Preciat G, Danielsdottir AD, Krecke M, Merten D, Haraldsdottir HS, Heinken A, Heirendt L, Magnusdottir S, Ravcheev DA, Sahoo S, Gawron P, Friscioni L, Garcia B, Prendergast M, Puente A, Rodrigues M, Roy A, Rouquaya M, Wiltgen L, Zagare A, John E, Krueger M, Kuperstein I, Zinovyev A, Schneider R, Fleming RMT, Thiele I: The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease. Nucleic Acids Res. 2019 Jan 8;47(D1):D614-D624. doi: 10.1093/nar/gky992. [PubMed:30371894 ]
Wishart DS, Li C, Marcu A, Badran H, Pon A, Budinski Z, Patron J, Lipton D, Cao X, Oler E, Li K, Paccoud M, Hong C, Guo AC, Chan C, Wei W, Ramirez-Gaona M: PathBank: a comprehensive pathway database for model organisms. Nucleic Acids Res. 2020 Jan 8;48(D1):D470-D478. doi: 10.1093/nar/gkz861. [PubMed:31602464 ]
Bansal P, Morgat A, Axelsen KB, Muthukrishnan V, Coudert E, Aimo L, Hyka-Nouspikel N, Gasteiger E, Kerhornou A, Neto TB, Pozzato M, Blatter MC, Ignatchenko A, Redaschi N, Bridge A: Rhea, the reaction knowledgebase in 2022. Nucleic Acids Res. 2022 Jan 7;50(D1):D693-D700. doi: 10.1093/nar/gkab1016. [PubMed:34755880 ]

Showing metabocard for D-Glycero-D-manno-heptose 1-phosphate (MMDBc0031604)

MOL for #<Metabolite:0x0000564abed4d578>

3D MOL for #<Metabolite:0x0000564abed4d578>

3D SDF for #<Metabolite:0x0000564abed4d578>

3D-SDF for #<Metabolite:0x0000564abed4d578>

PDB for #<Metabolite:0x0000564abed4d578>

3D PDB for #<Metabolite:0x0000564abed4d578>

SMILES for #<Metabolite:0x0000564abed4d578>

INCHI for #<Metabolite:0x0000564abed4d578>

Structure for #<Metabolite:0x0000564abed4d578>

3D Structure for #<Metabolite:0x0000564abed4d578>