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Showing NP-Card for Penitricin D (NP0003250)

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Record Information
Version2.0
Created at2020-12-09 00:32:20 UTC
Updated at2021-07-15 16:45:54 UTC
NP-MRD IDNP0003250
Secondary Accession NumbersNone
Natural Product Identification
Common NamePenitricin D
Provided ByNPAtlasNPAtlas Logo
Description Penitricin D is found in Aspergillus. Penitricin D was first documented in 2000 (PMID: 10805569). Based on a literature review very few articles have been published on 2-hydroxy-3-methylidenecyclopropan-1-one.
Structure
Data?1624573770
MOL3D MOLSDF3D SDFPDBSMILESInChI

MOL for NP0003250 (Penitricin D)


  Mrv1652306242117463D          

 10 10  0  0  0  0            999 V2000
    1.7457   -0.1807   -0.1703 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4344   -0.2882   -0.0290 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8732   -0.8885   -0.2622 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4325   -1.8435   -0.8918 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8169    0.2431    0.5868 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.1180    1.5340    0.1718 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2661   -0.8918   -0.7983 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2741    0.6088    0.3390 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8360    0.1394    1.7111 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6435    1.5674   -0.6572 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  3  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  2  1  0  0  0  0
  1  7  1  0  0  0  0
  1  8  1  0  0  0  0
  5  9  1  1  0  0  0
  6 10  1  0  0  0  0
M  END
Download

3D MOL for NP0003250 (Penitricin D)

     RDKit          3D

 10 10  0  0  0  0  0  0  0  0999 V2000
    1.7457   -0.1807   -0.1703 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4344   -0.2882   -0.0290 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8732   -0.8885   -0.2622 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4325   -1.8435   -0.8918 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8169    0.2431    0.5868 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.1180    1.5340    0.1718 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2661   -0.8918   -0.7983 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2741    0.6088    0.3390 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8360    0.1394    1.7111 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6435    1.5674   -0.6572 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  3
  2  3  1  0
  3  4  2  0
  3  5  1  0
  5  6  1  0
  5  2  1  0
  1  7  1  0
  1  8  1  0
  5  9  1  1
  6 10  1  0
M  END
Download

3D SDF for NP0003250 (Penitricin D)


  Mrv1652306242117463D          

 10 10  0  0  0  0            999 V2000
    1.7457   -0.1807   -0.1703 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4344   -0.2882   -0.0290 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8732   -0.8885   -0.2622 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4325   -1.8435   -0.8918 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8169    0.2431    0.5868 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.1180    1.5340    0.1718 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2661   -0.8918   -0.7983 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2741    0.6088    0.3390 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8360    0.1394    1.7111 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6435    1.5674   -0.6572 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  3  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  2  1  0  0  0  0
  1  7  1  0  0  0  0
  1  8  1  0  0  0  0
  5  9  1  1  0  0  0
  6 10  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0003250

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C4H4O2/c1-2-3(5)4(2)6/h3,5H,1H2/t3-/m1/s1

> <INCHI_KEY>
RWCLCTYWAIRJIL-UHFFFAOYSA-N

> <FORMULA>
C4H4O2

> <MOLECULAR_WEIGHT>
84.074

> <EXACT_MASS>
84.021129369

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
10

> <JCHEM_AVERAGE_POLARIZABILITY>
7.675305007500988

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R)-2-hydroxy-3-methylidenecyclopropan-1-one

> <ALOGPS_LOGP>
-0.62

> <JCHEM_LOGP>
-0.10936254166666667

> <ALOGPS_LOGS>
0.66

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.071487952566931

> <JCHEM_PKA_STRONGEST_ACIDIC>
10.17933359057506

> <JCHEM_PKA_STRONGEST_BASIC>
-3.7403080656569907

> <JCHEM_POLAR_SURFACE_AREA>
37.3

> <JCHEM_REFRACTIVITY>
20.1605

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.84e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2R)-2-hydroxy-3-methylidenecyclopropan-1-one

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for NP0003250 (Penitricin D)

     RDKit          3D

 10 10  0  0  0  0  0  0  0  0999 V2000
    1.7457   -0.1807   -0.1703 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4344   -0.2882   -0.0290 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8732   -0.8885   -0.2622 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4325   -1.8435   -0.8918 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8169    0.2431    0.5868 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.1180    1.5340    0.1718 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2661   -0.8918   -0.7983 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2741    0.6088    0.3390 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8360    0.1394    1.7111 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6435    1.5674   -0.6572 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  3
  2  3  1  0
  3  4  2  0
  3  5  1  0
  5  6  1  0
  5  2  1  0
  1  7  1  0
  1  8  1  0
  5  9  1  1
  6 10  1  0
M  END
Download

PDB for NP0003250 (Penitricin D)

HEADER    PROTEIN                                 24-JUN-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-JUN-21         0                                  
HETATM    1  C   UNK     0       1.746  -0.181  -0.170  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.434  -0.288  -0.029  0.00  0.00           C+0
HETATM    3  C   UNK     0      -0.873  -0.889  -0.262  0.00  0.00           C+0
HETATM    4  O   UNK     0      -1.433  -1.843  -0.892  0.00  0.00           O+0
HETATM    5  C   UNK     0      -0.817   0.243   0.587  0.00  0.00           C+0
HETATM    6  O   UNK     0      -1.118   1.534   0.172  0.00  0.00           O+0
HETATM    7  H   UNK     0       2.266  -0.892  -0.798  0.00  0.00           H+0
HETATM    8  H   UNK     0       2.274   0.609   0.339  0.00  0.00           H+0
HETATM    9  H   UNK     0      -0.836   0.139   1.711  0.00  0.00           H+0
HETATM   10  H   UNK     0      -1.644   1.567  -0.657  0.00  0.00           H+0
CONECT    1    2    7    8                                                  
CONECT    2    1    3    5                                                  
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6    2    9                                             
CONECT    6    5   10                                                       
CONECT    7    1                                                            
CONECT    8    1                                                            
CONECT    9    5                                                            
CONECT   10    6                                                            
MASTER        0    0    0    0    0    0    0    0   10    0   20    0
END
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3D PDB for NP0003250 (Penitricin D)

Download
SMILES for NP0003250 (Penitricin D)
[H]O[C@@]1([H])C(=O)C1=C([H])[H]
Download
INCHI for NP0003250 (Penitricin D)
InChI=1S/C4H4O2/c1-2-3(5)4(2)6/h3,5H,1H2/t3-/m1/s1
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View in JSmolView NMR Assignments
Synonyms
ValueSource
Penitricin-DMeSH
Chemical FormulaC4H4O2
Average Mass84.0740 Da
Monoisotopic Mass84.02113 Da
IUPAC Name(2R)-2-hydroxy-3-methylidenecyclopropan-1-one
Traditional Name(2R)-2-hydroxy-3-methylidenecyclopropan-1-one
CAS Registry NumberNot Available
SMILES
OC1C(=C)C1=O
InChI Identifier
InChI=1S/C4H4O2/c1-2-3(5)4(2)6/h3,5H,1H2
InChI KeyRWCLCTYWAIRJIL-UHFFFAOYSA-N
Experimental Spectra
Not Available
Predicted Spectra
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 25 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 252 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 50 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 75 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 101 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 126 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 151 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 176 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 201 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 226 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
AspergillusNPAtlas
Species Where Detected
Species NameSourceReference
Aspergillus nigerKNApSAcK Database
Chemical Taxonomy
ClassificationNot classified
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-0.62ALOGPS
logP-0.11ChemAxon
logS0.66ALOGPS
pKa (Strongest Acidic)10.18ChemAxon
pKa (Strongest Basic)-3.7ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count2ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area37.3 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity20.16 m³·mol⁻¹ChemAxon
Polarizability7.68 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleNoChemAxon
NPAtlas IDNPA015715  
HMDB IDNot Available
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID8232996  
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound10057442  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. Alvi KA, Nair BG, Rabenstein J, Davis G, Baker DD: CD45 tyrosine phosphatase inhibitory components from Aspergillus niger. J Antibiot (Tokyo). 2000 Feb;53(2):110-3. doi: 10.7164/antibiotics.53.110. [PubMed:10805569  ]