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Showing NP-Card for tulipalin b (NP0160615)

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Record Information
Version1.0
Created at2022-09-02 18:36:01 UTC
Updated at2022-09-02 18:36:01 UTC
NP-MRD IDNP0160615
Secondary Accession NumbersNone
Natural Product Identification
Common Nametulipalin b
DescriptionTulipalin B belongs to the class of organic compounds known as gamma butyrolactones. Gamma butyrolactones are compounds containing a gamma butyrolactone moiety, which consists of an aliphatic five-member ring with four carbon atoms, one oxygen atom, and bears a ketone group on the carbon adjacent to the oxygen atom. Tulipalin B 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. tulipalin b is found in Artabotrys hexapetalus. It was first documented in 2010 (PMID: 19939419). Based on a literature review a significant number of articles have been published on tulipalin B (PMID: 29475400) (PMID: 28485211) (PMID: 25126881) (PMID: 24317075) (PMID: 21512240) (PMID: 25997073).
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0160615 (tulipalin b)


  Mrv1652309022220362D          

  8  8  0  0  1  0            999 V2000
    0.5678    1.9393    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.1143    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2352    0.6294    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0198    0.8843    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9803   -0.1553    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1553   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0997    0.6294    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.8843    0.8843    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
  3  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  2  7  1  0  0  0  0
  7  8  1  6  0  0  0
M  END
Download

3D MOL for NP0160615 (tulipalin b)

     RDKit          3D

 14 14  0  0  0  0  0  0  0  0999 V2000
    1.8527   -0.4227   -0.4223 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7111    0.1747   -0.1577 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4599    1.5087    0.3798 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3671    2.3385    0.6392 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9335    1.6662    0.5396 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4219    0.3481    0.7259 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6407   -0.4066   -0.3581 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.6716   -1.7706   -0.1594 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8195    0.0219   -0.2676 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8461   -1.4250   -0.8217 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0510   -0.0314    1.7026 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5019    0.2657    0.5911 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0805   -0.0810   -1.3201 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7553   -2.1866   -1.0713 H   0  0  0  0  0  0  0  0  0  0  0  0
  8  7  1  0
  7  6  1  0
  6  5  1  0
  5  3  1  0
  3  4  2  0
  3  2  1  0
  2  1  2  3
  2  7  1  0
  8 14  1  0
  7 13  1  6
  6 11  1  0
  6 12  1  0
  1  9  1  0
  1 10  1  0
M  END
Download

3D SDF for NP0160615 (tulipalin b)


  Mrv1652309022220362D          

  8  8  0  0  1  0            999 V2000
    0.5678    1.9393    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.1143    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2352    0.6294    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0198    0.8843    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9803   -0.1553    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1553   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0997    0.6294    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.8843    0.8843    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
  3  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  2  7  1  0  0  0  0
  7  8  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0160615

> <DATABASE_NAME>
NP-MRD

> <SMILES>
O[C@H]1COC(=O)C1=C

> <INCHI_IDENTIFIER>
InChI=1S/C5H6O3/c1-3-4(6)2-8-5(3)7/h4,6H,1-2H2/t4-/m0/s1

> <INCHI_KEY>
BFLSLERVRLOFCX-BYPYZUCNSA-N

> <FORMULA>
C5H6O3

> <MOLECULAR_WEIGHT>
114.1

> <EXACT_MASS>
114.031694053

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
14

> <JCHEM_AVERAGE_POLARIZABILITY>
10.256059126212492

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(4R)-4-hydroxy-3-methylideneoxolan-2-one

> <ALOGPS_LOGP>
-0.38

> <JCHEM_LOGP>
-0.08480385866666675

> <ALOGPS_LOGS>
0.58

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.534215364831866

> <JCHEM_PKA_STRONGEST_BASIC>
-3.4399341994225416

> <JCHEM_POLAR_SURFACE_AREA>
46.53

> <JCHEM_REFRACTIVITY>
25.893499999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.38e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(4R)-4-hydroxy-3-methylideneoxolan-2-one

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0160615 (tulipalin b)

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PDB for NP0160615 (tulipalin b)
HEADER    PROTEIN                                 02-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   02-SEP-22         0                                  
HETATM    1  C   UNK     0       1.060   3.620   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.060   2.080   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.306   1.175   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       3.770   1.651   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0       1.830  -0.290   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       0.290  -0.290   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -0.186   1.175   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      -1.651   1.651   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    7                                                  
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    2    8                                                  
CONECT    8    7                                                            
MASTER        0    0    0    0    0    0    0    0    8    0   16    0
END

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3D PDB for NP0160615 (tulipalin b)
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SMILES for NP0160615 (tulipalin b)
O[C@H]1COC(=O)C1=C
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INCHI for NP0160615 (tulipalin b)
InChI=1S/C5H6O3/c1-3-4(6)2-8-5(3)7/h4,6H,1-2H2/t4-/m0/s1
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View in JSmol
Synonyms
ValueSource
(+)-Tulipalin bChEBI
2-Methylene-3-hydroxy-gamma-butyrolactoneChEBI
alpha-Methylene-beta-hydroxy-gamma-butyrolactoneChEBI
2-Methylene-3-hydroxy-g-butyrolactoneGenerator
2-Methylene-3-hydroxy-γ-butyrolactoneGenerator
a-Methylene-b-hydroxy-g-butyrolactoneGenerator
Α-methylene-β-hydroxy-γ-butyrolactoneGenerator
Chemical FormulaC5H6O3
Average Mass114.1000 Da
Monoisotopic Mass114.03169 Da
IUPAC NameNot Available
Traditional NameNot Available
CAS Registry NumberNot Available
SMILES
O[C@H]1COC(=O)C1=C
InChI Identifier
InChI=1S/C5H6O3/c1-3-4(6)2-8-5(3)7/h4,6H,1-2H2/t4-/m0/s1
InChI KeyBFLSLERVRLOFCX-BYPYZUCNSA-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 Origin
Species NameSourceReference
Artabotrys hexapetalusLOTUS Database
Chemical Taxonomy
Description Belongs to the class of organic compounds known as gamma butyrolactones. Gamma butyrolactones are compounds containing a gamma butyrolactone moiety, which consists of an aliphatic five-member ring with four carbon atoms, one oxygen atom, and bears a ketone group on the carbon adjacent to the oxygen atom.
KingdomOrganic compounds  
Super ClassOrganoheterocyclic compounds  
ClassLactones  
Sub ClassGamma butyrolactones  
Direct ParentGamma butyrolactones  
Alternative Parents
Substituents
  • Gamma butyrolactone
    • 

  • Tetrahydrofuran
    • 

  • Enoate ester
    • 

  • Alpha,beta-unsaturated carboxylic ester
    • 

  • Carboxylic acid ester
    • 

  • Secondary alcohol
    • 

  • Monocarboxylic acid or derivatives
    • 

  • Carboxylic acid derivative
    • 

  • Oxacycle
    • 

  • Organic oxide
    • 

  • Organooxygen compound
    • 

  • Organic oxygen compound
    • 

  • Alcohol
    • 

  • Carbonyl group
    • 

  • Hydrocarbon derivative
    • 

  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External Descriptors
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-0.38ALOGPS
logS0.58ALOGPS
HMDB IDNot Available
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDC00036320  
Chemspider ID8278669  
KEGG Compound IDNot Available
BioCyc IDCPD-18287  
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound10103141  
PDB IDNot Available
ChEBI ID87123  
Good Scents IDNot Available
References
General References
  1. Nomura T, Kuchida R, Kitaoka N, Kato Y: Molecular diversity of tuliposide B-converting enzyme in tulip (Tulipa gesneriana): identification of the third isozyme with a distinct expression profile. Biosci Biotechnol Biochem. 2018 May;82(5):810-820. doi: 10.1080/09168451.2018.1438170. Epub 2018 Feb 23. [PubMed:29475400  ] 
  2. Nomura T, Ueno A, Ogita S, Kato Y: Molecular diversity of tuliposide B-converting enzyme in tulip (Tulipa gesneriana): identification of the root-specific isozyme. Biosci Biotechnol Biochem. 2017 Jun;81(6):1185-1193. doi: 10.1080/09168451.2017.1295806. Epub 2017 Feb 28. [PubMed:28485211  ] 
  3. Nomura T, Hayashi E, Kawakami S, Ogita S, Kato Y: Environmentally benign process for the preparation of antimicrobial alpha-methylene-beta-hydroxy-gamma-butyrolactone (tulipalin B) from tulip biomass. Biosci Biotechnol Biochem. 2015;79(1):25-35. doi: 10.1080/09168451.2014.946395. Epub 2014 Aug 15. [PubMed:25126881  ] 
  4. Shigetomi K, Olesen SH, Yang Y, Mitsuhashi S, Schonbrunn E, Ubukata M: MurA as a primary target of tulipalin B and 6-tuliposide B. Biosci Biotechnol Biochem. 2013;77(12):2517-9. doi: 10.1271/bbb.130663. Epub 2013 Dec 7. [PubMed:24317075  ] 
  5. Shigetomi K, Omoto S, Kato Y, Ubukata M: Asymmetric total synthesis of 6-Tuliposide B and its biological activities against tulip pathogenic fungi. Biosci Biotechnol Biochem. 2011;75(4):718-22. doi: 10.1271/bbb.100845. Epub 2011  Apr 22. [PubMed:21512240  ] 
  6. Shigetomi K, Shoji K, Mitsuhashi S, Ubukata M: The antibacterial properties of 6-tuliposide B. Synthesis of 6-tuliposide B analogues and structure-activity relationship. Phytochemistry. 2010 Feb;71(2-3):312-24. doi: 10.1016/j.phytochem.2009.10.008.  Epub 2009 Nov 24. [PubMed:19939419  ] 
  7. Nomura T, Murase T, Ogita S, Kato Y: Molecular identification of tuliposide B-converting enzyme: a lactone-forming carboxylesterase from the pollen of tulip. Plant J. 2015 Jul;83(2):252-62. doi: 10.1111/tpj.12883. Epub 2015 Jun 12. [PubMed:25997073  ] 
  8. LOTUS database [Link]