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Showing NP-Card for methyl 2-(1-carbamimidoylpyrrolidin-2-yl)acetate (NP0259008)

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Record Information
Version2.0
Created at2022-09-08 00:43:42 UTC
Updated at2022-09-08 00:43:42 UTC
NP-MRD IDNP0259008
Secondary Accession NumbersNone
Natural Product Identification
Common Namemethyl 2-(1-carbamimidoylpyrrolidin-2-yl)acetate
DescriptionCimipronidine methyl ester 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. methyl 2-(1-carbamimidoylpyrrolidin-2-yl)acetate is found in Actaea racemosa. methyl 2-(1-carbamimidoylpyrrolidin-2-yl)acetate was first documented in 2009 (PMID: 19220011). Based on a literature review very few articles have been published on Cimipronidine methyl ester.
Structure
Thumb
MOL3D MOLSDFPDBSMILESInChI

MOL for NP0259008 (methyl 2-(1-carbamimidoylpyrrolidin-2-yl)acetate)


  Mrv1652309082202432D          

 13 13  0  0  0  0            999 V2000
    1.9967    3.5893    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2822    3.1768    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2822    2.3518    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9967    1.9393    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    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  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
    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
   -0.8843    0.8843    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4974    0.3323    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0558    1.6913    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
  3  4  2  0  0  0  0
  3  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
  6 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  2  0  0  0  0
 11 13  1  0  0  0  0
M  END
Download

3D MOL for NP0259008 (methyl 2-(1-carbamimidoylpyrrolidin-2-yl)acetate)

     RDKit          3D

 28 28  0  0  0  0  0  0  0  0999 V2000
   -1.9858    1.9503   -2.2764 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7021    1.0946   -1.7963 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5289    0.9958   -0.5213 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7699    2.1771    0.2337 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1358   -0.1980    0.1216 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0483   -0.9255    1.0255 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8824   -2.3390    0.4644 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5381   -2.3623   -0.2295 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0302   -0.9927    0.1536 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.1458   -0.6956   -0.7519 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8456    0.5727   -0.5726 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1736    1.6389   -0.6357 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2084    0.7336   -0.3317 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.7568    2.0359   -0.1755 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1504    2.9966    0.0706 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5246    2.2836    0.9443 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0684   -0.5624    0.9916 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5479   -0.8442    2.0287 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9175   -3.0373    1.3259 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7218   -2.5590   -0.2119 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6367   -2.4680   -1.3272 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1088   -3.1709    0.1446 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3649   -1.1192    1.2077 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9105   -1.5155   -0.6132 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8382   -0.7826   -1.8122 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9435    2.2193    0.9002 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0928    2.8008   -0.6048 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7396    2.0729   -0.7042 H   0  0  0  0  0  0  0  0  0  0  0  0
 14 13  1  0
 13 11  1  0
 11 12  2  0
 11 10  1  0
 10  9  1  0
  9  8  1  0
  8  7  1  0
  7  6  1  0
  6  5  1  0
  5  3  1  0
  3  4  1  0
  3  2  2  0
  5  9  1  0
 14 26  1  0
 14 27  1  0
 14 28  1  0
 10 24  1  0
 10 25  1  0
  9 23  1  1
  8 21  1  0
  8 22  1  0
  7 19  1  0
  7 20  1  0
  6 17  1  0
  6 18  1  0
  4 15  1  0
  4 16  1  0
  2  1  1  0
M  END
Download

3D SDF for NP0259008 (methyl 2-(1-carbamimidoylpyrrolidin-2-yl)acetate)


  Mrv1652309082202432D          

 13 13  0  0  0  0            999 V2000
    1.9967    3.5893    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2822    3.1768    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2822    2.3518    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9967    1.9393    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    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  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
    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
   -0.8843    0.8843    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4974    0.3323    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0558    1.6913    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
  3  4  2  0  0  0  0
  3  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
  6 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  2  0  0  0  0
 11 13  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0259008

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC(=O)CC1CCCN1C(N)=N

> <INCHI_IDENTIFIER>
InChI=1S/C8H15N3O2/c1-13-7(12)5-6-3-2-4-11(6)8(9)10/h6H,2-5H2,1H3,(H3,9,10)

> <INCHI_KEY>
XDCKHCPSQTVMKR-UHFFFAOYSA-N

> <FORMULA>
C8H15N3O2

> <MOLECULAR_WEIGHT>
185.227

> <EXACT_MASS>
185.116426735

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
28

> <JCHEM_AVERAGE_POLARIZABILITY>
19.30629795292196

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
methyl 2-(1-carbamimidoylpyrrolidin-2-yl)acetate

> <JCHEM_LOGP>
-0.37079891300000023

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_BASIC>
12.4977144691979

> <JCHEM_POLAR_SURFACE_AREA>
79.41

> <JCHEM_REFRACTIVITY>
58.6924

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
methyl (1-carbamimidoylpyrrolidin-2-yl)acetate

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0259008 (methyl 2-(1-carbamimidoylpyrrolidin-2-yl)acetate)

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PDB for NP0259008 (methyl 2-(1-carbamimidoylpyrrolidin-2-yl)acetate)
HEADER    PROTEIN                                 08-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   08-SEP-22         0                                  
HETATM    1  C   UNK     0       3.727   6.700   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0       2.393   5.930   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0       2.393   4.390   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       3.727   3.620   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       1.060   3.620   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.060   2.080   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       2.306   1.175   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       1.830  -0.290   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       0.290  -0.290   0.000  0.00  0.00           C+0
HETATM   10  N   UNK     0      -0.186   1.175   0.000  0.00  0.00           N+0
HETATM   11  C   UNK     0      -1.651   1.651   0.000  0.00  0.00           C+0
HETATM   12  N   UNK     0      -2.795   0.620   0.000  0.00  0.00           N+0
HETATM   13  N   UNK     0      -1.971   3.157   0.000  0.00  0.00           N+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6                                                       
CONECT    6    5    7   10                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9    6   11                                                  
CONECT   11   10   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11                                                            
MASTER        0    0    0    0    0    0    0    0   13    0   26    0
END

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3D PDB for NP0259008 (methyl 2-(1-carbamimidoylpyrrolidin-2-yl)acetate)
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SMILES for NP0259008 (methyl 2-(1-carbamimidoylpyrrolidin-2-yl)acetate)
COC(=O)CC1CCCN1C(N)=N
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INCHI for NP0259008 (methyl 2-(1-carbamimidoylpyrrolidin-2-yl)acetate)
InChI=1S/C8H15N3O2/c1-13-7(12)5-6-3-2-4-11(6)8(9)10/h6H,2-5H2,1H3,(H3,9,10)
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View in JSmol
SynonymsNot Available
Chemical FormulaC8H15N3O2
Average Mass185.2270 Da
Monoisotopic Mass185.11643 Da
IUPAC Namemethyl 2-(1-carbamimidoylpyrrolidin-2-yl)acetate
Traditional Namemethyl (1-carbamimidoylpyrrolidin-2-yl)acetate
CAS Registry NumberNot Available
SMILES
COC(=O)CC1CCCN1C(N)=N
InChI Identifier
InChI=1S/C8H15N3O2/c1-13-7(12)5-6-3-2-4-11(6)8(9)10/h6H,2-5H2,1H3,(H3,9,10)
InChI KeyXDCKHCPSQTVMKR-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
Actaea racemosaLOTUS 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
    • 

  • Methyl ester
    • 

  • Carboxylic acid ester
    • 

  • Guanidine
    • 

  • Carboxylic acid derivative
    • 

  • Monocarboxylic acid or derivatives
    • 

  • Carboximidamide
    • 

  • Azacycle
    • 

  • Organooxygen compound
    • 

  • Organonitrogen compound
    • 

  • Carbonyl group
    • 

  • Imine
    • 

  • Organic oxygen compound
    • 

  • Organic oxide
    • 

  • Hydrocarbon derivative
    • 

  • Organic nitrogen compound
    • 

  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic 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-0.37ChemAxon
pKa (Strongest Basic)12.5ChemAxon
Physiological Charge1ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area79.41 ŲChemAxon
Rotatable Bond Count3ChemAxon
Refractivity58.69 m³·mol⁻¹ChemAxon
Polarizability19.31 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDNot Available
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID96352633  
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound101467166  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. Godecke T, Lankin DC, Nikolic D, Chen SN, van Breemen RB, Farnsworth NR, Pauli GF: Guanidine alkaloids and Pictet-Spengler adducts from black cohosh (Cimicifuga racemosa). J Nat Prod. 2009 Mar 27;72(3):433-7. doi: 10.1021/np8006952. [PubMed:19220011  ] 
  2. LOTUS database [Link]