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Showing NP-Card for (r)-2-methylpyrrolidine (NP0182983)

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Record Information
Version2.0
Created at2022-09-03 21:48:55 UTC
Updated at2022-09-03 21:48:55 UTC
NP-MRD IDNP0182983
Secondary Accession NumbersNone
Natural Product Identification
Common Name(r)-2-methylpyrrolidine
Description(R)-2-methylpyrrolidine belongs to the class of organic compounds known as pyrrolidines. Pyrrolidines are compounds containing a pyrrolidine ring, which is a five-membered saturated aliphatic heterocycle with one nitrogen atom and four carbon atoms. (r)-2-methylpyrrolidine is found in Apis cerana. (r)-2-methylpyrrolidine was first documented in 2020 (PMID: 32155676). Based on a literature review very few articles have been published on (R)-2-methylpyrrolidine (PMID: 34142836).
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0182983 ((r)-2-methylpyrrolidine)


  Mrv1652309032223482D          

  6  6  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  2  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
    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 N   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  6  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
  2  6  1  0  0  0  0
M  END
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3D MOL for NP0182983 ((r)-2-methylpyrrolidine)

     RDKit          3D

 17 17  0  0  0  0  0  0  0  0999 V2000
    2.0750   -0.1888    0.0886 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6806   -0.0815   -0.4189 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.0978    1.0502    0.2139 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5212    0.7011   -0.2133 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5091   -0.7989   -0.0951 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1363   -1.2302   -0.1956 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.4911   -1.1856   -0.1301 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7083    0.5364   -0.4891 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1949   -0.0155    1.1681 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7128    0.1156   -1.5065 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0485    1.0522    1.3102 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2245    2.0131   -0.2269 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5933    0.9815   -1.2822 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2795    1.1908    0.4137 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0857   -1.2399   -0.9407 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9823   -1.0605    0.8660 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1667   -1.8401    0.5830 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  2  1  0
  1  7  1  0
  1  8  1  0
  1  9  1  0
  2 10  1  6
  3 11  1  0
  3 12  1  0
  4 13  1  0
  4 14  1  0
  5 15  1  0
  5 16  1  0
  6 17  1  0
M  END
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3D SDF for NP0182983 ((r)-2-methylpyrrolidine)


  Mrv1652309032223482D          

  6  6  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  2  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
    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 N   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  6  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
  2  6  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0182983

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@@H]1CCCN1

> <INCHI_IDENTIFIER>
InChI=1S/C5H11N/c1-5-3-2-4-6-5/h5-6H,2-4H2,1H3/t5-/m1/s1

> <INCHI_KEY>
RGHPCLZJAFCTIK-RXMQYKEDSA-N

> <FORMULA>
C5H11N

> <MOLECULAR_WEIGHT>
85.15

> <EXACT_MASS>
85.089149358

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
17

> <JCHEM_AVERAGE_POLARIZABILITY>
10.56776256215846

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R)-2-methylpyrrolidine

> <JCHEM_LOGP>
0.6294940196666664

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_BASIC>
11.464525311701982

> <JCHEM_POLAR_SURFACE_AREA>
12.03

> <JCHEM_REFRACTIVITY>
26.6532

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(2R)-2-methylpyrrolidine

> <JCHEM_VEBER_RULE>
1

$$$$
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3D-SDF for NP0182983 ((r)-2-methylpyrrolidine)

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PDB for NP0182983 ((r)-2-methylpyrrolidine)
HEADER    PROTEIN                                 03-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   03-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  C   UNK     0       1.830  -0.290   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.290  -0.290   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0      -0.186   1.175   0.000  0.00  0.00           N+0
CONECT    1    2                                                            
CONECT    2    1    3    6                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    2                                                       
MASTER        0    0    0    0    0    0    0    0    6    0   12    0
END

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3D PDB for NP0182983 ((r)-2-methylpyrrolidine)
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SMILES for NP0182983 ((r)-2-methylpyrrolidine)
C[C@@H]1CCCN1
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INCHI for NP0182983 ((r)-2-methylpyrrolidine)
InChI=1S/C5H11N/c1-5-3-2-4-6-5/h5-6H,2-4H2,1H3/t5-/m1/s1
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View in JSmol
SynonymsNot Available
Chemical FormulaC5H11N
Average Mass85.1500 Da
Monoisotopic Mass85.08915 Da
IUPAC Name(2R)-2-methylpyrrolidine
Traditional Name(2R)-2-methylpyrrolidine
CAS Registry NumberNot Available
SMILES
C[C@@H]1CCCN1
InChI Identifier
InChI=1S/C5H11N/c1-5-3-2-4-6-5/h5-6H,2-4H2,1H3/t5-/m1/s1
InChI KeyRGHPCLZJAFCTIK-RXMQYKEDSA-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
Apis ceranaLOTUS Database
Chemical Taxonomy
Description Belongs to the class of organic compounds known as pyrrolidines. Pyrrolidines are compounds containing a pyrrolidine ring, which is a five-membered saturated aliphatic heterocycle with one nitrogen atom and four carbon atoms.
KingdomOrganic compounds  
Super ClassOrganoheterocyclic compounds  
ClassPyrrolidines  
Sub ClassNot Available
Direct ParentPyrrolidines  
Alternative Parents
Substituents
  • Pyrrolidine
    • 

  • Azacycle
    • 

  • Secondary amine
    • 

  • Secondary aliphatic amine
    • 

  • Organic nitrogen compound
    • 

  • Organopnictogen compound
    • 

  • Hydrocarbon derivative
    • 

  • Organonitrogen compound
    • 

  • Amine
    • 

  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External Descriptors
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
logP0.63ChemAxon
pKa (Strongest Basic)11.46ChemAxon
Physiological Charge1ChemAxon
Hydrogen Acceptor Count1ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area12.03 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity26.65 m³·mol⁻¹ChemAxon
Polarizability10.57 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleNoChemAxon
HMDB IDNot Available
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID556822  
KEGG Compound IDNot Available
BioCyc IDCPD-16509  
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound641544  
PDB IDNot Available
ChEBI ID78858  
Good Scents IDNot Available
References
General References
  1. Craft CL, Lemler PM, Vaccaro PH: Optical Activity in Saturated Cyclic Amines: Untangling the Roles of Nitrogen-Inversion and Ring-Puckering Dynamics. J Phys Chem A. 2021 Jul 1;125(25):5562-5584. doi: 10.1021/acs.jpca.1c03882. Epub  2021 Jun 18. [PubMed:34142836  ] 
  2. Zablocki J, Arteaga O, Balzer F, Hertel D, Holstein JJ, Clever G, Anhauser J, Puttreddy R, Rissanen K, Meerholz K, Lutzen A, Schiek M: Polymorphic chiral squaraine crystallites in textured thin films. Chirality. 2020 May;32(5):619-631. doi: 10.1002/chir.23213. Epub 2020 Mar 10. [PubMed:32155676  ] 
  3. LOTUS database [Link]