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Showing NP-Card for Penitricin (NP0021888)

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Record Information
Version2.0
Created at2021-01-06 07:08:07 UTC
Updated at2021-07-15 17:37:34 UTC
NP-MRD IDNP0021888
Secondary Accession NumbersNone
Natural Product Identification
Common NamePenitricin
Provided ByNPAtlasNPAtlas Logo
Description Penitricin is found in Penicillium, Penicillium aculeatum NR 5165 and Talaromyces aculeatus. Penitricin was first documented in 1984 (PMID: 6547944). Based on a literature review very few articles have been published on 2-(hydroxymethyl)cyclopropan-1-one.
Structure
Data?1624506967
MOL3D MOLSDF3D SDFPDBSMILESInChI

MOL for NP0021888 (Penitricin)


  Mrv1652306242105193D          

 12 12  0  0  0  0            999 V2000
   -1.7826    1.1506   -1.6411 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2884    0.5526   -0.6833 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3341   -0.4227    0.3899 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.1333    0.3748    0.1803 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.1273   -0.2745   -0.3439 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.0915   -0.3350    0.6601 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4034   -1.4871    0.0580 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9237   -0.2290    1.3311 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0592    1.2071    0.8897 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8733   -1.3427   -0.5875 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5150    0.1965   -1.2551 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1994    0.6094    1.0019 H   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  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  4  2  1  0  0  0  0
  3  7  1  0  0  0  0
  3  8  1  0  0  0  0
  4  9  1  1  0  0  0
  5 10  1  0  0  0  0
  5 11  1  0  0  0  0
  6 12  1  0  0  0  0
M  END
Download

3D MOL for NP0021888 (Penitricin)

     RDKit          3D

 12 12  0  0  0  0  0  0  0  0999 V2000
   -1.7826    1.1506   -1.6411 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2884    0.5526   -0.6833 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3341   -0.4227    0.3899 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1333    0.3748    0.1803 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.1273   -0.2745   -0.3439 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0915   -0.3350    0.6601 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4034   -1.4871    0.0580 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9237   -0.2290    1.3311 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0592    1.2071    0.8897 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8733   -1.3427   -0.5875 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5150    0.1965   -1.2551 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1994    0.6094    1.0019 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  4  2  1  0
  3  7  1  0
  3  8  1  0
  4  9  1  1
  5 10  1  0
  5 11  1  0
  6 12  1  0
M  END
Download

3D SDF for NP0021888 (Penitricin)


  Mrv1652306242105193D          

 12 12  0  0  0  0            999 V2000
   -1.7826    1.1506   -1.6411 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2884    0.5526   -0.6833 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3341   -0.4227    0.3899 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.1333    0.3748    0.1803 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.1273   -0.2745   -0.3439 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.0915   -0.3350    0.6601 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4034   -1.4871    0.0580 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9237   -0.2290    1.3311 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0592    1.2071    0.8897 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8733   -1.3427   -0.5875 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5150    0.1965   -1.2551 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1994    0.6094    1.0019 H   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  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  4  2  1  0  0  0  0
  3  7  1  0  0  0  0
  3  8  1  0  0  0  0
  4  9  1  1  0  0  0
  5 10  1  0  0  0  0
  5 11  1  0  0  0  0
  6 12  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0021888

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C4H6O2/c5-2-3-1-4(3)6/h3,5H,1-2H2/t3-/m0/s1

> <INCHI_KEY>
CERKMQPAWBVDBC-UHFFFAOYSA-N

> <FORMULA>
C4H6O2

> <MOLECULAR_WEIGHT>
86.09

> <EXACT_MASS>
86.036779433

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
12

> <JCHEM_AVERAGE_POLARIZABILITY>
8.273474404060519

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S)-2-(hydroxymethyl)cyclopropan-1-one

> <ALOGPS_LOGP>
-1.20

> <JCHEM_LOGP>
-0.5832966086666667

> <ALOGPS_LOGS>
0.98

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
16.239045373481353

> <JCHEM_PKA_STRONGEST_ACIDIC>
14.381974349196778

> <JCHEM_PKA_STRONGEST_BASIC>
-2.6679109426471195

> <JCHEM_POLAR_SURFACE_AREA>
37.3

> <JCHEM_REFRACTIVITY>
20.793599999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
8.16e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2S)-2-(hydroxymethyl)cyclopropan-1-one

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for NP0021888 (Penitricin)

     RDKit          3D

 12 12  0  0  0  0  0  0  0  0999 V2000
   -1.7826    1.1506   -1.6411 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2884    0.5526   -0.6833 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3341   -0.4227    0.3899 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1333    0.3748    0.1803 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.1273   -0.2745   -0.3439 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0915   -0.3350    0.6601 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4034   -1.4871    0.0580 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9237   -0.2290    1.3311 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0592    1.2071    0.8897 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8733   -1.3427   -0.5875 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5150    0.1965   -1.2551 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1994    0.6094    1.0019 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  4  2  1  0
  3  7  1  0
  3  8  1  0
  4  9  1  1
  5 10  1  0
  5 11  1  0
  6 12  1  0
M  END
Download

PDB for NP0021888 (Penitricin)

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  O   UNK     0      -1.783   1.151  -1.641  0.00  0.00           O+0
HETATM    2  C   UNK     0      -1.288   0.553  -0.683  0.00  0.00           C+0
HETATM    3  C   UNK     0      -1.334  -0.423   0.390  0.00  0.00           C+0
HETATM    4  C   UNK     0      -0.133   0.375   0.180  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.127  -0.275  -0.344  0.00  0.00           C+0
HETATM    6  O   UNK     0       2.091  -0.335   0.660  0.00  0.00           O+0
HETATM    7  H   UNK     0      -1.403  -1.487   0.058  0.00  0.00           H+0
HETATM    8  H   UNK     0      -1.924  -0.229   1.331  0.00  0.00           H+0
HETATM    9  H   UNK     0       0.059   1.207   0.890  0.00  0.00           H+0
HETATM   10  H   UNK     0       0.873  -1.343  -0.588  0.00  0.00           H+0
HETATM   11  H   UNK     0       1.515   0.197  -1.255  0.00  0.00           H+0
HETATM   12  H   UNK     0       2.199   0.609   1.002  0.00  0.00           H+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2    4    7    8                                             
CONECT    4    3    5    2    9                                             
CONECT    5    4    6   10   11                                             
CONECT    6    5   12                                                       
CONECT    7    3                                                            
CONECT    8    3                                                            
CONECT    9    4                                                            
CONECT   10    5                                                            
CONECT   11    5                                                            
CONECT   12    6                                                            
MASTER        0    0    0    0    0    0    0    0   12    0   24    0
END
Download

3D PDB for NP0021888 (Penitricin)

Download
SMILES for NP0021888 (Penitricin)
[H]OC([H])([H])[C@@]1([H])C(=O)C1([H])[H]
Download
INCHI for NP0021888 (Penitricin)
InChI=1S/C4H6O2/c5-2-3-1-4(3)6/h3,5H,1-2H2/t3-/m0/s1
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View in JSmolView NMR Assignments
SynonymsNot Available
Chemical FormulaC4H6O2
Average Mass86.0900 Da
Monoisotopic Mass86.03678 Da
IUPAC Name(2S)-2-(hydroxymethyl)cyclopropan-1-one
Traditional Name(2S)-2-(hydroxymethyl)cyclopropan-1-one
CAS Registry NumberNot Available
SMILES
OCC1CC1=O
InChI Identifier
InChI=1S/C4H6O2/c5-2-3-1-4(3)6/h3,5H,1-2H2
InChI KeyCERKMQPAWBVDBC-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
PenicilliumNPAtlas
Penicillium aculeatum NR 5165Fungi
Talaromyces aculeatusLOTUS 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-1.2ALOGPS
logP-0.58ChemAxon
logS0.98ALOGPS
pKa (Strongest Acidic)14.38ChemAxon
pKa (Strongest Basic)-2.7ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count2ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area37.3 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity20.79 m³·mol⁻¹ChemAxon
Polarizability8.27 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleNoChemAxon
NPAtlas IDNPA020911  
HMDB IDNot Available
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID78436030  
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound56635971  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. Okuda T, Yoneyama Y, Fujiwara A, Furumai T: Penitricin, a new class of antibiotic produced by Penicillium aculeatum. I. Taxonomy of the producer strain and fermentation. J Antibiot (Tokyo). 1984 Jul;37(7):712-7. doi: 10.7164/antibiotics.37.712. [PubMed:6547944  ]