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Showing NP-Card for Antibiotic PA 4046I (NP0062108)

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Record Information
Version1.0
Created at2022-04-28 06:46:33 UTC
Updated at2022-04-28 06:46:33 UTC
NP-MRD IDNP0062108
Secondary Accession NumbersNone
Natural Product Identification
Common NameAntibiotic PA 4046I
DescriptionCyclopropaneacetic acid, alpha-amino-1-methyl-, (S)- belongs to the class of organic compounds known as l-alpha-amino acids. These are alpha amino acids which have the L-configuration of the alpha-carbon atom. Antibiotic PA 4046I is found in Micromonospora miyakonensis sp. nov. PA-4046. It was first documented in 2008 (PMID: 18755563). Based on a literature review very few articles have been published on Cyclopropaneacetic acid, alpha-amino-1-methyl-, (S)-.
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0062108 (Antibiotic PA 4046I)


  Mrv1652304282208462D          

  9  9  0  0  1  0            999 V2000
   -0.1743    0.1743    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2382    0.8888    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6507    0.1743    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2350    1.5646    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7114    1.5646    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.5332    1.4927    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0064    2.1685    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8819    0.7450    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3627    2.3123    0.0000 N   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
  1  3  1  0  0  0  0
  2  4  1  0  0  0  0
  2  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  6  8  1  0  0  0  0
  5  9  1  6  0  0  0
M  END
Download

3D MOL for NP0062108 (Antibiotic PA 4046I)

     RDKit          3D

 20 20  0  0  0  0  0  0  0  0999 V2000
   -1.3696   -0.1900    1.1839 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6005   -0.1034   -0.1106 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.5678    0.8792   -0.1157 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.2136    0.8604   -1.4135 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.5644    0.5537    0.9077 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7593    0.3153    0.5838 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2823    0.4845    2.2662 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5039   -1.3549   -0.9138 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3946   -0.2007   -1.3603 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3715   -0.6246    1.0606 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8041   -0.8969    1.8550 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4763    0.8054    1.6691 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1608    1.9234    0.0234 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9186    0.0733   -1.3696 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8146    1.7364   -1.4434 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4277   -0.3624    2.8018 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9900   -2.2674   -0.5022 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3974   -1.5165   -1.5244 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1086    0.3374   -2.2836 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4872   -0.4519   -1.3146 H   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  1
  2  8  1  0
  8  9  1  0
  2  3  1  0
  3  4  1  0
  3  5  1  0
  5  7  1  0
  5  6  2  0
  9  2  1  0
  1 10  1  0
  1 11  1  0
  1 12  1  0
  8 17  1  0
  8 18  1  0
  9 19  1  0
  9 20  1  0
  3 13  1  1
  4 14  1  0
  4 15  1  0
  7 16  1  0
M  END
Download

3D SDF for NP0062108 (Antibiotic PA 4046I)


  Mrv1652304282208462D          

  9  9  0  0  1  0            999 V2000
   -0.1743    0.1743    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2382    0.8888    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6507    0.1743    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2350    1.5646    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7114    1.5646    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.5332    1.4927    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0064    2.1685    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8819    0.7450    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3627    2.3123    0.0000 N   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
  1  3  1  0  0  0  0
  2  4  1  0  0  0  0
  2  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  6  8  1  0  0  0  0
  5  9  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0062108

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C6H11NO2/c1-6(2-3-6)4(7)5(8)9/h4H,2-3,7H2,1H3,(H,8,9)/t4-/m1/s1

> <INCHI_KEY>
BCTQUNGXIVZUSB-SCSAIBSYSA-N

> <FORMULA>
C6H11NO2

> <MOLECULAR_WEIGHT>
129.159

> <EXACT_MASS>
129.078978598

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
20

> <JCHEM_AVERAGE_POLARIZABILITY>
13.231698348361101

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S)-2-amino-2-(1-methylcyclopropyl)acetic acid

> <ALOGPS_LOGP>
-2.39

> <JCHEM_LOGP>
-2.038677764536592

> <ALOGPS_LOGS>
0.08

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.5146749698840627

> <JCHEM_PKA_STRONGEST_BASIC>
9.302319714037818

> <JCHEM_POLAR_SURFACE_AREA>
63.31999999999999

> <JCHEM_REFRACTIVITY>
32.0888

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.56e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(S)-amino(1-methylcyclopropyl)acetic acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0062108 (Antibiotic PA 4046I)

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PDB for NP0062108 (Antibiotic PA 4046I)
HEADER    PROTEIN                                 28-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   28-APR-22         0                                  
HETATM    1  C   UNK     0      -0.325   0.325   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.445   1.659   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.215   0.325   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -0.439   2.921   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.328   2.921   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.862   2.786   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       3.745   4.048   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       3.513   1.391   0.000  0.00  0.00           O+0
HETATM    9  N   UNK     0       0.677   4.316   0.000  0.00  0.00           N+0
CONECT    1    2    3                                                       
CONECT    2    1    3    4    5                                             
CONECT    3    2    1                                                       
CONECT    4    2                                                            
CONECT    5    2    6    9                                                  
CONECT    6    5    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6                                                            
CONECT    9    5                                                            
MASTER        0    0    0    0    0    0    0    0    9    0   18    0
END

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3D PDB for NP0062108 (Antibiotic PA 4046I)
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SMILES for NP0062108 (Antibiotic PA 4046I)
CC1(CC1)[C@H](N)C(O)=O
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INCHI for NP0062108 (Antibiotic PA 4046I)
InChI=1S/C6H11NO2/c1-6(2-3-6)4(7)5(8)9/h4H,2-3,7H2,1H3,(H,8,9)/t4-/m1/s1
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View in JSmol
SynonymsNot Available
Chemical FormulaC6H11NO2
Average Mass129.1590 Da
Monoisotopic Mass129.07898 Da
IUPAC Name(2S)-2-amino-2-(1-methylcyclopropyl)acetic acid
Traditional Name(S)-amino(1-methylcyclopropyl)acetic acid
CAS Registry NumberNot Available
SMILES
CC1(CC1)[C@H](N)C(O)=O
InChI Identifier
InChI=1S/C6H11NO2/c1-6(2-3-6)4(7)5(8)9/h4H,2-3,7H2,1H3,(H,8,9)/t4-/m1/s1
InChI KeyBCTQUNGXIVZUSB-SCSAIBSYSA-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
Micromonospora miyakonensis sp. nov. PA-4046Bacteria
Chemical Taxonomy
Description Belongs to the class of organic compounds known as l-alpha-amino acids. These are alpha amino acids which have the L-configuration of the alpha-carbon atom.
KingdomOrganic compounds  
Super ClassOrganic acids and derivatives  
ClassCarboxylic acids and derivatives  
Sub ClassAmino acids, peptides, and analogues  
Direct ParentL-alpha-amino acids  
Alternative Parents
Substituents
  • L-alpha-amino acid
    • 

  • Amino acid
    • 

  • Monocarboxylic acid or derivatives
    • 

  • Carboxylic acid
    • 

  • Organic nitrogen compound
    • 

  • Organic oxygen compound
    • 

  • Organic oxide
    • 

  • Hydrocarbon derivative
    • 

  • Primary amine
    • 

  • Organooxygen compound
    • 

  • Organonitrogen compound
    • 

  • Primary aliphatic amine
    • 

  • Carbonyl group
    • 

  • Amine
    • 

  • 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
logP-2.4ALOGPS
logP-2ChemAxon
logS0.08ALOGPS
pKa (Strongest Acidic)2.51ChemAxon
pKa (Strongest Basic)9.3ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area63.32 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity32.09 m³·mol⁻¹ChemAxon
Polarizability13.23 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 ID2321441  
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound3060518  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. Saravanan M, Siva Kumari K, Pratap Reddy P, Naidu MN, Moses Babu J, Srivastava AK, Lakshmi Kumar T, Chandra Sekhar BV, Satyanarayana B: Identification, synthesis, isolation and spectral characterization of potential impurities of montelukast sodium. J Pharm Biomed Anal. 2008 Nov 4;48(3):708-15. doi: 10.1016/j.jpba.2008.07.007. Epub 2008 Jul 16. [PubMed:18755563  ]