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Showing NP-Card for 4-(buta-1,3-diyn-1-yl)cyclopent-4-ene-1,3-diol (NP0323558)

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Record Information
Version2.0
Created at2022-09-12 03:03:37 UTC
Updated at2022-09-12 03:03:37 UTC
NP-MRD IDNP0323558
Secondary Accession NumbersNone
Natural Product Identification
Common Name4-(buta-1,3-diyn-1-yl)cyclopent-4-ene-1,3-diol
Description4-(Buta-1,3-diyn-1-yl)cyclopent-4-ene-1,3-diol belongs to the class of organic compounds known as secondary alcohols. Secondary alcohols are compounds containing a secondary alcohol functional group, with the general structure HOC(R)(R') (R,R'=alkyl, aryl). 4-(buta-1,3-diyn-1-yl)cyclopent-4-ene-1,3-diol is found in Sistotrema raduloides. 4-(Buta-1,3-diyn-1-yl)cyclopent-4-ene-1,3-diol is an extremely weak basic (essentially neutral) compound (based on its pKa).
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0323558 (4-(buta-1,3-diyn-1-yl)cyclopent-4-ene-1,3-diol)


  Mrv1533004251511382D          

 11 11  0  0  0  0            999 V2000
    0.5678    1.9393    0.0000 O   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
    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 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  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
   -0.8146   -1.4901    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2995   -2.1576    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7844   -2.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  4  6  1  0  0  0  0
  6  7  2  0  0  0  0
  2  7  1  0  0  0  0
  6  8  1  0  0  0  0
  8  9  3  0  0  0  0
  9 10  1  0  0  0  0
 10 11  3  0  0  0  0
M  END
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3D MOL for NP0323558 (4-(buta-1,3-diyn-1-yl)cyclopent-4-ene-1,3-diol)

     RDKit          3D

 19 19  0  0  0  0  0  0  0  0999 V2000
    5.2320   -1.1398    0.8093 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0659   -0.8944    0.6033 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7015   -0.5850    0.3731 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5426   -0.3047    0.1886 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1436    0.0511   -0.0164 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2779    1.0532   -0.7538 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7504    1.1801   -0.7827 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.1325    2.2587   -0.0184 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1865   -0.1388   -0.1858 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9883   -0.6511    0.5652 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.9106   -2.0310    0.4038 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.2592   -1.3426    0.9983 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3424    1.7730   -1.3255 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0478    1.2731   -1.8522 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4497    2.9968   -0.0323 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5412   -0.8143   -0.9693 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0380    0.0767    0.4926 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1302   -0.3925    1.6405 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8340   -2.3683    0.1920 H   0  0  0  0  0  0  0  0  0  0  0  0
  8  7  1  0
  7  9  1  0
  9 10  1  0
 10 11  1  0
 10  5  1  0
  5  6  2  0
  5  4  1  0
  4  3  3  0
  3  2  1  0
  2  1  3  0
  6  7  1  0
  8 15  1  0
  7 14  1  6
  9 16  1  0
  9 17  1  0
 10 18  1  1
 11 19  1  0
  6 13  1  0
  1 12  1  0
M  END
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3D SDF for NP0323558 (4-(buta-1,3-diyn-1-yl)cyclopent-4-ene-1,3-diol)


  Mrv1533004251511382D          

 11 11  0  0  0  0            999 V2000
    0.5678    1.9393    0.0000 O   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
    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 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  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
   -0.8146   -1.4901    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2995   -2.1576    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7844   -2.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  4  6  1  0  0  0  0
  6  7  2  0  0  0  0
  2  7  1  0  0  0  0
  6  8  1  0  0  0  0
  8  9  3  0  0  0  0
  9 10  1  0  0  0  0
 10 11  3  0  0  0  0
M  END
> <DATABASE_ID>
NP0323558

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC1CC(O)C(=C1)C#CC#C

> <INCHI_IDENTIFIER>
InChI=1S/C9H8O2/c1-2-3-4-7-5-8(10)6-9(7)11/h1,5,8-11H,6H2

> <INCHI_KEY>
CJQQKSVOADEXIS-UHFFFAOYSA-N

> <FORMULA>
C9H8O2

> <MOLECULAR_WEIGHT>
148.161

> <EXACT_MASS>
148.052429498

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
19

> <JCHEM_AVERAGE_POLARIZABILITY>
15.812485359694712

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
4-(buta-1,3-diyn-1-yl)cyclopent-4-ene-1,3-diol

> <ALOGPS_LOGP>
0.14

> <JCHEM_LOGP>
-0.31887530400000014

> <ALOGPS_LOGS>
-2.85

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.939258769186857

> <JCHEM_PKA_STRONGEST_ACIDIC>
14.018180076705569

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9172273778134343

> <JCHEM_POLAR_SURFACE_AREA>
40.46

> <JCHEM_REFRACTIVITY>
43.017

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.07e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
4-(buta-1,3-diyn-1-yl)cyclopent-4-ene-1,3-diol

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0323558 (4-(buta-1,3-diyn-1-yl)cyclopent-4-ene-1,3-diol)

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PDB for NP0323558 (4-(buta-1,3-diyn-1-yl)cyclopent-4-ene-1,3-diol)
HEADER    PROTEIN                                 25-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   25-APR-15         0                                  
HETATM    1  O   UNK     0       1.060   3.620   0.000  0.00  0.00           O+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  C   UNK     0       1.830  -0.290   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       2.735  -1.536   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  C   UNK     0      -0.615  -1.536   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -1.521  -2.782   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -2.426  -4.027   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -3.331  -5.273   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3    7                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4    7    8                                                  
CONECT    7    6    2                                                       
CONECT    8    6    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10                                                            
MASTER        0    0    0    0    0    0    0    0   11    0   22    0
END

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3D PDB for NP0323558 (4-(buta-1,3-diyn-1-yl)cyclopent-4-ene-1,3-diol)
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SMILES for NP0323558 (4-(buta-1,3-diyn-1-yl)cyclopent-4-ene-1,3-diol)
OC1CC(O)C(=C1)C#CC#C
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INCHI for NP0323558 (4-(buta-1,3-diyn-1-yl)cyclopent-4-ene-1,3-diol)
InChI=1S/C9H8O2/c1-2-3-4-7-5-8(10)6-9(7)11/h1,5,8-11H,6H2
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View in JSmol
SynonymsNot Available
Chemical FormulaC9H8O2
Average Mass148.1610 Da
Monoisotopic Mass148.05243 Da
IUPAC Name4-(buta-1,3-diyn-1-yl)cyclopent-4-ene-1,3-diol
Traditional Name4-(buta-1,3-diyn-1-yl)cyclopent-4-ene-1,3-diol
CAS Registry NumberNot Available
SMILES
OC1CC(O)C(=C1)C#CC#C
InChI Identifier
InChI=1S/C9H8O2/c1-2-3-4-7-5-8(10)6-9(7)11/h1,5,8-11H,6H2
InChI KeyCJQQKSVOADEXIS-UHFFFAOYSA-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
Sistotrema raduloidesLOTUS Database
Chemical Taxonomy
Description Belongs to the class of organic compounds known as secondary alcohols. Secondary alcohols are compounds containing a secondary alcohol functional group, with the general structure HOC(R)(R') (R,R'=alkyl, aryl).
KingdomOrganic compounds  
Super ClassOrganic oxygen compounds  
ClassOrganooxygen compounds  
Sub ClassAlcohols and polyols  
Direct ParentSecondary alcohols  
Alternative Parents
Substituents
  • Secondary alcohol
    • 

  • Acetylide
    • 

  • 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
logP0.14ALOGPS
logP-0.32ChemAxon
logS-2.8ALOGPS
pKa (Strongest Acidic)14.02ChemAxon
pKa (Strongest Basic)-2.9ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count2ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area40.46 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity43.02 m³·mol⁻¹ChemAxon
Polarizability15.81 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 IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound71435535  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. LOTUS database [Link]