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Showing NP-Card for valienone (NP0236226)

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Record Information
Version2.0
Created at2022-09-06 19:03:58 UTC
Updated at2022-09-06 19:03:59 UTC
NP-MRD IDNP0236226
Secondary Accession NumbersNone
Natural Product Identification
Common Namevalienone
DescriptionValienone belongs to the class of organic compounds known as cyclohexenones. Cyclohexenones are compounds containing a cylohexenone moiety, which is a six-membered aliphatic ring that carries a ketone and has one endocyclic double bond. Valienone is a secondary metabolite. Secondary metabolites are metabolically or physiologically non-essential metabolites that may serve a role as defense or signalling molecules. In some cases they are simply molecules that arise from the incomplete metabolism of other secondary metabolites. valienone was first documented in 2001 (PMID: 11456959). Based on a literature review a significant number of articles have been published on valienone (PMID: 31940432) (PMID: 30857183) (PMID: 29103465) (PMID: 28367638) (PMID: 26436873) (PMID: 23879653).
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0236226 (valienone)


  Mrv1652309062221032D          

 12 12  0  0  1  0            999 V2000
    0.7145    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 C   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   -0.4125    0.0000 C   0  0  1  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
    0.0000    0.0000    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  1  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  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  4  7  1  0  0  0  0
  7  8  1  1  0  0  0
  7  9  1  0  0  0  0
  9 10  1  6  0  0  0
  9 11  1  0  0  0  0
  2 11  1  0  0  0  0
 11 12  1  1  0  0  0
M  END
Download

3D MOL for NP0236226 (valienone)

     RDKit          3D

 22 22  0  0  0  0  0  0  0  0999 V2000
   -0.2643   -2.7558   -1.3399 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3429   -1.6243   -0.8016 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7545   -0.6702   -0.7528 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6757    0.4627   -0.0814 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8247    1.3963   -0.0670 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8560    0.8610   -0.8255 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5699    0.8362    0.6813 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.3934    1.5809   -0.1630 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2022   -0.4529    1.1196 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.2096   -1.2277    1.7209 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6280   -1.1861   -0.1565 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.2589   -0.2944   -1.0372 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6822   -0.9020   -1.2947 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1415    1.5389    1.0030 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5711    2.3876   -0.4948 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2837    0.1021   -0.3784 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2852    1.4761    1.5570 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8024    2.0417   -0.8127 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0614   -0.3132    1.8016 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4710   -0.6850    2.1784 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2721   -2.0293    0.0992 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9702   -0.5426   -1.9553 H   0  0  0  0  0  0  0  0  0  0  0  0
  6  5  1  0
  5  4  1  0
  4  3  2  0
  3  2  1  0
  2  1  2  0
  2 11  1  0
 11 12  1  0
 11  9  1  0
  9 10  1  0
  9  7  1  0
  7  8  1  0
  7  4  1  0
  6 16  1  0
  5 14  1  0
  5 15  1  0
  3 13  1  0
 11 21  1  1
 12 22  1  0
  9 19  1  1
 10 20  1  0
  7 17  1  1
  8 18  1  0
M  END
Download

3D SDF for NP0236226 (valienone)


  Mrv1652309062221032D          

 12 12  0  0  1  0            999 V2000
    0.7145    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 C   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   -0.4125    0.0000 C   0  0  1  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
    0.0000    0.0000    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  1  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  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  4  7  1  0  0  0  0
  7  8  1  1  0  0  0
  7  9  1  0  0  0  0
  9 10  1  6  0  0  0
  9 11  1  0  0  0  0
  2 11  1  0  0  0  0
 11 12  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0236226

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OCC1=CC(=O)[C@H](O)[C@@H](O)[C@@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C7H10O5/c8-2-3-1-4(9)6(11)7(12)5(3)10/h1,5-8,10-12H,2H2/t5-,6+,7+/m1/s1

> <INCHI_KEY>
WQMTVIWUDHFWNR-VQVTYTSYSA-N

> <FORMULA>
C7H10O5

> <MOLECULAR_WEIGHT>
174.152

> <EXACT_MASS>
174.052823422

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
22

> <JCHEM_AVERAGE_POLARIZABILITY>
15.844582479411148

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(4R,5S,6R)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-one

> <JCHEM_LOGP>
-2.416357805333333

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.637267039247707

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.693559204925387

> <JCHEM_PKA_STRONGEST_BASIC>
-2.7843409452702508

> <JCHEM_POLAR_SURFACE_AREA>
97.99000000000001

> <JCHEM_REFRACTIVITY>
39.4586

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(4R,5S,6R)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-one

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0236226 (valienone)

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PDB for NP0236226 (valienone)
HEADER    PROTEIN                                 06-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-SEP-22         0                                  
HETATM    1  O   UNK     0       1.334   3.850   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.667  -0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       4.001  -2.310   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       1.334  -2.310   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      -1.334  -0.770   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0      -1.334   2.310   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   11                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5    7                                                  
CONECT    5    4    6                                                       
CONECT    6    5                                                            
CONECT    7    4    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9    2   12                                                  
CONECT   12   11                                                            
MASTER        0    0    0    0    0    0    0    0   12    0   24    0
END

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3D PDB for NP0236226 (valienone)
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SMILES for NP0236226 (valienone)
OCC1=CC(=O)[C@H](O)[C@@H](O)[C@@H]1O
Download
INCHI for NP0236226 (valienone)
InChI=1S/C7H10O5/c8-2-3-1-4(9)6(11)7(12)5(3)10/h1,5-8,10-12H,2H2/t5-,6+,7+/m1/s1
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View in JSmol
SynonymsNot Available
Chemical FormulaC7H10O5
Average Mass174.1520 Da
Monoisotopic Mass174.05282 Da
IUPAC Name(4R,5S,6R)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-one
Traditional Name(4R,5S,6R)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-one
CAS Registry NumberNot Available
SMILES
OCC1=CC(=O)[C@H](O)[C@@H](O)[C@@H]1O
InChI Identifier
InChI=1S/C7H10O5/c8-2-3-1-4(9)6(11)7(12)5(3)10/h1,5-8,10-12H,2H2/t5-,6+,7+/m1/s1
InChI KeyWQMTVIWUDHFWNR-VQVTYTSYSA-N
Experimental Spectra
Not Available
Predicted Spectra
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 25 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 100 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 252 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 1000 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 50 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 200 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 75 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 300 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 101 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 126 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 151 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 176 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 700 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 201 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 800 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 226 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 900 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Chemical Shift Submissions
Not Available
Species
Species of OriginNot Available
Chemical Taxonomy
Description Belongs to the class of organic compounds known as cyclohexenones. Cyclohexenones are compounds containing a cylohexenone moiety, which is a six-membered aliphatic ring that carries a ketone and has one endocyclic double bond.
KingdomOrganic compounds  
Super ClassOrganic oxygen compounds  
ClassOrganooxygen compounds  
Sub ClassCarbonyl compounds  
Direct ParentCyclohexenones  
Alternative Parents
Substituents
  • Cyclohexenone
    • 

  • Cyclitol or derivatives
    • 

  • Secondary alcohol
    • 

  • Polyol
    • 

  • Organic oxide
    • 

  • Hydrocarbon derivative
    • 

  • Primary alcohol
    • 

  • Alcohol
    • 

  • Aliphatic homomonocyclic compound
Molecular FrameworkAliphatic homomonocyclic compounds
External DescriptorsNot Available
Physical Properties
StateNot Available
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP-2.4ChemAxon
pKa (Strongest Acidic)11.69ChemAxon
pKa (Strongest Basic)-2.8ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area97.99 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity39.46 m³·mol⁻¹ChemAxon
Polarizability15.84 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDNot Available
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID9291675  
KEGG Compound IDNot Available
BioCyc IDCPD-9665  
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound11116543  
PDB IDNot Available
ChEBI ID111521  
Good Scents IDNot Available
References
General References
  1. Cui L, Wei X, Wang X, Bai L, Lin S, Feng Y: A Validamycin Shunt Pathway for Valienamine Synthesis in Engineered Streptomyces hygroscopicus 5008. ACS Synth Biol. 2020 Feb 21;9(2):294-303. doi: 10.1021/acssynbio.9b00319. Epub 2020 Jan 24. [PubMed:31940432  ] 
  2. Liu Y, Wan Y, Zhu J, Li M, Yu Z, Han J, Zhang Z, Han W: Exploration of Catalytic Selectivity for Aminotransferase (BtrR) Based on Multiple Molecular Dynamics Simulations. Int J Mol Sci. 2019 Mar 8;20(5). pii: ijms20051188. doi: 10.3390/ijms20051188. [PubMed:30857183  ] 
  3. Cui L, Yanagi K, Shi T, Liu ZM, Bai LQ, Feng Y: A quantitative analytical method for valienone and its application in the evaluation of valienone production by a breakthrough microbial process. Chin J Nat Med. 2017 Oct;15(10):794-800. doi: 10.1016/S1875-5364(17)30111-5. [PubMed:29103465  ] 
  4. Cui L, Guan XQ, Liu ZM, Fan LY, Li Q, Feng Y: A new pre-column derivatization for valienamine and beta-valienamine using o-phthalaldehyde to determine the epimeric purity by HPLC and application of this method to monitor enzymatic catalyzed synthesis of beta-valienamine. J Asian Nat Prod Res. 2017 Apr;19(4):347-357. doi: 10.1080/10286020.2017.1292257. [PubMed:28367638  ] 
  5. Cui L, Zhu Y, Guan X, Deng Z, Bai L, Feng Y: De Novo Biosynthesis of beta-Valienamine in Engineered Streptomyces hygroscopicus 5008. ACS Synth Biol. 2016 Jan 15;5(1):15-20. doi: 10.1021/acssynbio.5b00138. Epub 2015 Oct 13. [PubMed:26436873  ] 
  6. Mondal S, Prathap A, Sureshan KM: Vinylogy in orthoester hydrolysis: total syntheses of cyclophellitol, valienamine, gabosine K, valienone, gabosine G, 1-epi-streptol, streptol, and uvamalol A. J Org Chem. 2013 Aug 2;78(15):7690-700. doi: 10.1021/jo401272j. Epub 2013 Jul 24. [PubMed:23879653  ] 
  7. Sedmera P, Halada P, Pospisil S: New carbasugars from Streptomyces lincolnensis. Magn Reson Chem. 2009 Jun;47(6):519-22. doi: 10.1002/mrc.2408. [PubMed:19224545  ] 
  8. Minagawa K, Zhang Y, Ito T, Bai L, Deng Z, Mahmud T: ValC, a new type of C7-Cyclitol kinase involved in the biosynthesis of the antifungal agent validamycin A. Chembiochem. 2007 Apr 16;8(6):632-41. doi: 10.1002/cbic.200600528. [PubMed:17335096  ] 
  9. Dong H, Mahmud T, Tornus I, Lee S, Floss HG: Biosynthesis of the validamycins: identification of intermediates in the biosynthesis of validamycin A by Streptomyces hygroscopicus var. limoneus. J Am Chem Soc. 2001 Mar 28;123(12):2733-42. doi: 10.1021/ja003643n. [PubMed:11456959  ] 
  10. Mahmud T, Xu J, Choi YU: Synthesis of 5-epi-[6-(2)H(2)]valiolone and stereospecifically monodeuterated 5-epi-valiolones: exploring the steric course of 5-epi-valiolone dehydratase in validamycin A biosynthesis. J Org Chem. 2001 Jul 27;66(15):5066-73. doi: 10.1021/jo0101003. [PubMed:11463258  ] 
  11. LOTUS database [Link]