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Showing NP-Card for (1s)-2,3-dimethyl-5-methylidene-4-oxocyclopent-2-ene-1-carboxylic acid (NP0298625)

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Record Information
Version2.0
Created at2022-09-10 09:59:50 UTC
Updated at2022-09-10 09:59:51 UTC
NP-MRD IDNP0298625
Secondary Accession NumbersNone
Natural Product Identification
Common Name(1s)-2,3-dimethyl-5-methylidene-4-oxocyclopent-2-ene-1-carboxylic acid
DescriptionDesepoxy-4,5-didehydromethylenomycin A belongs to the class of organic compounds known as cyclic ketones. These are organic compounds containing a ketone that is conjugated to a cyclic moiety. (1s)-2,3-dimethyl-5-methylidene-4-oxocyclopent-2-ene-1-carboxylic acid is found in Streptomyces coelicolor. Based on a literature review very few articles have been published on Desepoxy-4,5-didehydromethylenomycin A.
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0298625 ((1s)-2,3-dimethyl-5-methylidene-4-oxocyclopent-2-ene-1-carboxylic acid)


  Mrv1652309102211592D          

 12 12  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 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4652   -0.8227    0.0000 C   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
   -0.3297   -0.8227    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 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4974    0.3323    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0558    1.6913    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
  5  7  2  0  0  0  0
  7  8  1  0  0  0  0
  7  9  1  0  0  0  0
  2  9  1  0  0  0  0
  9 10  1  6  0  0  0
 10 11  2  0  0  0  0
 10 12  1  0  0  0  0
M  END
Download

3D MOL for NP0298625 ((1s)-2,3-dimethyl-5-methylidene-4-oxocyclopent-2-ene-1-carboxylic acid)

     RDKit          3D

 22 22  0  0  0  0  0  0  0  0999 V2000
   -2.1521    1.2875    1.4314 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0320    0.7454    0.9443 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3107    1.3077    0.9983 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6348    2.4211    1.5258 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1834    0.3516    0.3380 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6521    0.5546    0.1804 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4909   -0.6870   -0.0838 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0600   -1.8750   -0.8113 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9248   -0.5514    0.2425 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.7927   -0.4572   -0.9605 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6777   -1.3296   -1.1323 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5943    0.5816   -1.8402 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0709    0.7377    1.3076 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1256    2.2409    1.9283 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8829    1.6387   -0.0282 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1164    0.2977    1.1572 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0671   -0.0757   -0.6312 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6871   -2.7736   -0.2396 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6297   -1.8850   -1.8118 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1506   -1.8911   -0.7964 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3055   -1.3572    0.9088 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1901    0.7183   -2.6272 H   0  0  0  0  0  0  0  0  0  0  0  0
  8  7  1  0
  7  5  2  0
  5  6  1  0
  5  3  1  0
  3  4  2  0
  3  2  1  0
  2  1  2  3
  2  9  1  0
  9 10  1  0
 10 12  1  0
 10 11  2  0
  9  7  1  0
  8 18  1  0
  8 19  1  0
  8 20  1  0
  6 15  1  0
  6 16  1  0
  6 17  1  0
  1 13  1  0
  1 14  1  0
  9 21  1  1
 12 22  1  0
M  END
Download

3D SDF for NP0298625 ((1s)-2,3-dimethyl-5-methylidene-4-oxocyclopent-2-ene-1-carboxylic acid)


  Mrv1652309102211592D          

 12 12  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 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4652   -0.8227    0.0000 C   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
   -0.3297   -0.8227    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 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4974    0.3323    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0558    1.6913    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
  5  7  2  0  0  0  0
  7  8  1  0  0  0  0
  7  9  1  0  0  0  0
  2  9  1  0  0  0  0
  9 10  1  6  0  0  0
 10 11  2  0  0  0  0
 10 12  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0298625

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC1=C(C)C(=O)C(=C)[C@H]1C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C9H10O3/c1-4-5(2)8(10)6(3)7(4)9(11)12/h7H,3H2,1-2H3,(H,11,12)/t7-/m0/s1

> <INCHI_KEY>
YVQOPMVVZGYOBC-ZETCQYMHSA-N

> <FORMULA>
C9H10O3

> <MOLECULAR_WEIGHT>
166.176

> <EXACT_MASS>
166.062994182

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
22

> <JCHEM_AVERAGE_POLARIZABILITY>
16.821007668691593

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(1S)-2,3-dimethyl-5-methylidene-4-oxocyclopent-2-ene-1-carboxylic acid

> <JCHEM_LOGP>
1.3544130130000003

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.245814782478656

> <JCHEM_PKA_STRONGEST_BASIC>
-6.374727270529523

> <JCHEM_POLAR_SURFACE_AREA>
54.370000000000005

> <JCHEM_REFRACTIVITY>
43.99660000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(1S)-2,3-dimethyl-5-methylidene-4-oxocyclopent-2-ene-1-carboxylic acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0298625 ((1s)-2,3-dimethyl-5-methylidene-4-oxocyclopent-2-ene-1-carboxylic acid)

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PDB for NP0298625 ((1s)-2,3-dimethyl-5-methylidene-4-oxocyclopent-2-ene-1-carboxylic acid)
HEADER    PROTEIN                                 10-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   10-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  C   UNK     0       1.830  -0.290   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.735  -1.536   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.290  -0.290   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -0.615  -1.536   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -0.186   1.175   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -1.651   1.651   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0      -2.795   0.620   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0      -1.971   3.157   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    9                                                  
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    2   10                                                  
CONECT   10    9   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10                                                            
MASTER        0    0    0    0    0    0    0    0   12    0   24    0
END

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3D PDB for NP0298625 ((1s)-2,3-dimethyl-5-methylidene-4-oxocyclopent-2-ene-1-carboxylic acid)
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SMILES for NP0298625 ((1s)-2,3-dimethyl-5-methylidene-4-oxocyclopent-2-ene-1-carboxylic acid)
CC1=C(C)C(=O)C(=C)[C@H]1C(O)=O
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INCHI for NP0298625 ((1s)-2,3-dimethyl-5-methylidene-4-oxocyclopent-2-ene-1-carboxylic acid)
InChI=1S/C9H10O3/c1-4-5(2)8(10)6(3)7(4)9(11)12/h7H,3H2,1-2H3,(H,11,12)/t7-/m0/s1
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View in JSmol
SynonymsNot Available
Chemical FormulaC9H10O3
Average Mass166.1760 Da
Monoisotopic Mass166.06299 Da
IUPAC Name(1S)-2,3-dimethyl-5-methylidene-4-oxocyclopent-2-ene-1-carboxylic acid
Traditional Name(1S)-2,3-dimethyl-5-methylidene-4-oxocyclopent-2-ene-1-carboxylic acid
CAS Registry NumberNot Available
SMILES
CC1=C(C)C(=O)C(=C)[C@H]1C(O)=O
InChI Identifier
InChI=1S/C9H10O3/c1-4-5(2)8(10)6(3)7(4)9(11)12/h7H,3H2,1-2H3,(H,11,12)/t7-/m0/s1
InChI KeyYVQOPMVVZGYOBC-ZETCQYMHSA-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
Streptomyces coelicolorLOTUS Database
Chemical Taxonomy
Description Belongs to the class of organic compounds known as cyclic ketones. These are organic compounds containing a ketone that is conjugated to a cyclic moiety.
KingdomOrganic compounds  
Super ClassOrganic oxygen compounds  
ClassOrganooxygen compounds  
Sub ClassCarbonyl compounds  
Direct ParentCyclic ketones  
Alternative Parents
Substituents
  • Cyclic ketone
    • 

  • Monocarboxylic acid or derivatives
    • 

  • Carboxylic acid
    • 

  • Carboxylic acid derivative
    • 

  • Organic oxide
    • 

  • Hydrocarbon derivative
    • 

  • 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
logP1.35ChemAxon
pKa (Strongest Acidic)4.25ChemAxon
pKa (Strongest Basic)-6.4ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area54.37 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity44 m³·mol⁻¹ChemAxon
Polarizability16.82 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDNot Available
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID78439770  
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound102509096  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. LOTUS database [Link]