NP-MRD: Showing NP-Card for (2s,3s,4r,5r,6s)-2,3,4,5,6,7-hexahydroxyheptanal (NP0289669)

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Record Information

Version

2.0

Created at

2022-09-09 19:58:22 UTC

Updated at

2022-09-09 19:58:22 UTC

NP-MRD ID

NP0289669

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(2s,3s,4r,5r,6s)-2,3,4,5,6,7-hexahydroxyheptanal

Description

Glycero-manno-Heptose belongs to the class of organic compounds known as heptoses. These are monosaccharides in which the sugar unit is a seven-carbon containing moeity. (2s,3s,4r,5r,6s)-2,3,4,5,6,7-hexahydroxyheptanal is found in Shigella flexneri. (2s,3s,4r,5r,6s)-2,3,4,5,6,7-hexahydroxyheptanal was first documented in 2005 (PMID: 16030223). Based on a literature review a small amount of articles have been published on glycero-manno-Heptose (PMID: 28063198) (PMID: 18657609) (PMID: 17241201).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309092221582D          

 14 13  0  0  1  0            999 V2000
    2.9980    2.5559    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.7125    2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4270    2.5559    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.4270    3.3809    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.1414    2.1434    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    5.1414    1.3184    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.8559    2.5559    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.8559    3.3809    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.5704    2.1434    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    6.5704    1.3184    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.2849    2.5559    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    7.2849    3.3809    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.9993    2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.7138    2.5559    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  1  0  0  0
  3  5  1  0  0  0  0
  5  6  1  6  0  0  0
  5  7  1  0  0  0  0
  7  8  1  6  0  0  0
  7  9  1  0  0  0  0
  9 10  1  1  0  0  0
  9 11  1  0  0  0  0
 11 12  1  1  0  0  0
 11 13  1  0  0  0  0
 13 14  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0289669

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C7H14O7/c8-1-3(10)5(12)7(14)6(13)4(11)2-9/h1,3-7,9-14H,2H2/t3-,4+,5-,6-,7+/m1/s1

> <INCHI_KEY>
YPZMPEPLWKRVLD-BIVRFLNRSA-N

> <FORMULA>
C7H14O7

> <MOLECULAR_WEIGHT>
210.182

> <EXACT_MASS>
210.073952791

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
28

> <JCHEM_AVERAGE_POLARIZABILITY>
18.70124780941255

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S,3S,4R,5R,6S)-2,3,4,5,6,7-hexahydroxyheptanal

> <JCHEM_LOGP>
-4.198695505

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.872874960059786

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.193377535156834

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9742118561862485

> <JCHEM_POLAR_SURFACE_AREA>
138.45000000000002

> <JCHEM_REFRACTIVITY>
43.308099999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
(2S,3S,4R,5R,6S)-2,3,4,5,6,7-hexahydroxyheptanal

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 09-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   09-SEP-22         0                                  
HETATM    1  O   UNK     0       5.596   4.771   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       6.930   4.001   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       8.264   4.771   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       8.264   6.311   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       9.597   4.001   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       9.597   2.461   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0      10.931   4.771   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      10.931   6.311   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0      12.265   4.001   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      12.265   2.461   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0      13.598   4.771   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0      13.598   6.311   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0      14.932   4.001   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0      16.266   4.771   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11   14                                                       
CONECT   14   13                                                            
MASTER        0    0    0    0    0    0    0    0   14    0   26    0
END

View in JSmol

Synonyms

Value	Source
D-Glycero-D-manno-heptose	MeSH
Glycero-manno-heptose, (D-glycero-D-manno)-isomer	MeSH
Glycero-manno-heptose, (D-glycero-L-manno)-isomer	MeSH
L-Glycero-D-manno-heptose	MeSH

Chemical Formula

C₇H₁₄O₇

Average Mass

210.1820 Da

Monoisotopic Mass

210.07395 Da

IUPAC Name

(2S,3S,4R,5R,6S)-2,3,4,5,6,7-hexahydroxyheptanal

Traditional Name

(2S,3S,4R,5R,6S)-2,3,4,5,6,7-hexahydroxyheptanal

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C7H14O7/c8-1-3(10)5(12)7(14)6(13)4(11)2-9/h1,3-7,9-14H,2H2/t3-,4+,5-,6-,7+/m1/s1

InChI Key

YPZMPEPLWKRVLD-BIVRFLNRSA-N

Experimental Spectra

Not Available

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 25 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Shigella flexneri	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as heptoses. These are monosaccharides in which the sugar unit is a seven-carbon containing moeity.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Heptoses

Alternative Parents

Substituents

Heptose monosaccharide
Medium-chain aldehyde
Beta-hydroxy aldehyde
Alpha-hydroxyaldehyde
Secondary alcohol
Polyol
Organic oxide
Hydrocarbon derivative
Primary alcohol
Carbonyl group
Aldehyde
Alcohol
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

Not Available

Physical Properties

State

Not Available

Experimental Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Predicted Properties

Property	Value	Source
logP	-4.2	ChemAxon
pKa (Strongest Acidic)	12.19	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	138.45 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	43.31 m³·mol⁻¹	ChemAxon
Polarizability	18.7 Å³	ChemAxon
Number of Rings	0	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

133263

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

151200

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Wierzbicki IH, Zielke RA, Korotkov KV, Sikora AE: Functional and structural studies on the Neisseria gonorrhoeae GmhA, the first enzyme in the glycero-manno-heptose biosynthesis pathways, demonstrate a critical role in lipooligosaccharide synthesis and gonococcal viability. Microbiologyopen. 2017 Apr;6(2):e00432. doi: 10.1002/mbo3.432. Epub 2017 Jan 7. [PubMed:28063198 ]
Charbonneau ME, Mourez M: The Escherichia coli AIDA-I autotransporter undergoes cytoplasmic glycosylation independently of export. Res Microbiol. 2008 Sep-Oct;159(7-8):537-44. doi: 10.1016/j.resmic.2008.06.009. Epub 2008 Jul 6. [PubMed:18657609 ]
Kim HS, Lee MA, Chun SJ, Park SJ, Lee KH: Role of NtrC in biofilm formation via controlling expression of the gene encoding an ADP-glycero-manno-heptose-6-epimerase in the pathogenic bacterium, Vibrio vulnificus. Mol Microbiol. 2007 Jan;63(2):559-74. doi: 10.1111/j.1365-2958.2006.05527.x. [PubMed:17241201 ]
McArthur F, Andersson CE, Loutet S, Mowbray SL, Valvano MA: Functional analysis of the glycero-manno-heptose 7-phosphate kinase domain from the bifunctional HldE protein, which is involved in ADP-L-glycero-D-manno-heptose biosynthesis. J Bacteriol. 2005 Aug;187(15):5292-300. doi: 10.1128/JB.187.15.5292-5300.2005. [PubMed:16030223 ]
LOTUS database [Link]

Showing NP-Card for (2s,3s,4r,5r,6s)-2,3,4,5,6,7-hexahydroxyheptanal (NP0289669)

MOL for NP0289669 ((2s,3s,4r,5r,6s)-2,3,4,5,6,7-hexahydroxyheptanal)

3D MOL for NP0289669 ((2s,3s,4r,5r,6s)-2,3,4,5,6,7-hexahydroxyheptanal)

3D SDF for NP0289669 ((2s,3s,4r,5r,6s)-2,3,4,5,6,7-hexahydroxyheptanal)

3D-SDF for NP0289669 ((2s,3s,4r,5r,6s)-2,3,4,5,6,7-hexahydroxyheptanal)

PDB for NP0289669 ((2s,3s,4r,5r,6s)-2,3,4,5,6,7-hexahydroxyheptanal)

3D PDB for NP0289669 ((2s,3s,4r,5r,6s)-2,3,4,5,6,7-hexahydroxyheptanal)

SMILES for NP0289669 ((2s,3s,4r,5r,6s)-2,3,4,5,6,7-hexahydroxyheptanal)

INCHI for NP0289669 ((2s,3s,4r,5r,6s)-2,3,4,5,6,7-hexahydroxyheptanal)

Structure for NP0289669 ((2s,3s,4r,5r,6s)-2,3,4,5,6,7-hexahydroxyheptanal)

3D Structure for NP0289669 ((2s,3s,4r,5r,6s)-2,3,4,5,6,7-hexahydroxyheptanal)