NP-MRD: Showing NP-Card for cimipronidine (NP0028440)

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Record Information

Version

2.0

Created at

2021-06-19 20:19:57 UTC

Updated at

2021-06-29 23:55:14 UTC

NP-MRD ID

NP0028440

Secondary Accession Numbers

None

Natural Product Identification

Common Name

cimipronidine

Provided By

JEOL Database JEOL Logo

Description

cimipronidine is found in Cimicifuga racemosa. cimipronidine was first documented in 2005 (Fabricant, D. S., et al.). Based on a literature review very few articles have been published on ZINC14684375.

Structure

MOL 3D MOL SDF 3D SDF PDB SMILES InChI


  Mrv1652306192122193D          

 25 25  0  0  0  0            999 V2000
    2.7455   -1.9164   -0.0234 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.7227   -1.2270    0.3647 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0924   -1.5325    1.5086 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.2424   -0.1652   -0.3368 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0547    0.4779   -0.1303 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.3568    1.1771   -1.4491 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.0234    1.5674   -1.9367 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.8699    0.3353   -1.5805 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.3409    0.7036   -1.4027 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.1943   -0.1205   -2.3269 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7772    0.3472   -3.2959 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2679   -1.4262   -1.9997 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8954   -2.6579    0.6712 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3780   -2.3097    2.0847 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4010   -0.9139    1.9018 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8464   -0.2415    0.1043 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0218    1.2039    0.6868 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8211    0.4760   -2.1531 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0250    2.0338   -1.3258 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0456    1.7901   -3.0076 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3635    2.4580   -1.3933 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7261   -0.4232   -2.3616 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5241    1.7528   -1.6664 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7104    0.5833   -0.3787 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6979   -1.6524   -1.2092 H   0  0  0  0  0  0  0  0  0  0  0  0
  4  2  1  0  0  0  0
  2  1  2  3  0  0  0
  8  7  1  0  0  0  0
  2  3  1  0  0  0  0
  7  6  1  0  0  0  0
  8  9  1  0  0  0  0
  6  5  1  0  0  0  0
  9 10  1  0  0  0  0
  5  4  1  0  0  0  0
 10 12  1  0  0  0  0
  4  8  1  0  0  0  0
 10 11  2  0  0  0  0
  8 22  1  6  0  0  0
  7 20  1  0  0  0  0
  7 21  1  0  0  0  0
  6 18  1  0  0  0  0
  6 19  1  0  0  0  0
  5 16  1  0  0  0  0
  5 17  1  0  0  0  0
  1 13  1  0  0  0  0
  3 14  1  0  0  0  0
  3 15  1  0  0  0  0
  9 23  1  0  0  0  0
  9 24  1  0  0  0  0
 12 25  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0028440

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C7H13N3O2/c8-7(9)10-3-1-2-5(10)4-6(11)12/h5H,1-4H2,(H3,8,9)(H,11,12)/t5-/m0/s1

> <INCHI_KEY>
VYKGYAQKCAHXKR-YFKPBYRVSA-N

> <FORMULA>
C7H13N3O2

> <MOLECULAR_WEIGHT>
171.2

> <EXACT_MASS>
171.100776671

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
25

> <JCHEM_AVERAGE_POLARIZABILITY>
17.461483572373723

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-[(2S)-1-carbamimidoylpyrrolidin-2-yl]acetic acid

> <ALOGPS_LOGP>
-1.07

> <JCHEM_LOGP>
-2.1616691190566626

> <ALOGPS_LOGS>
-1.75

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.064748844168099

> <JCHEM_PKA_STRONGEST_BASIC>
12.731855489128938

> <JCHEM_POLAR_SURFACE_AREA>
90.41000000000001

> <JCHEM_REFRACTIVITY>
53.923300000000005

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.02e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
[(2S)-1-carbamimidoylpyrrolidin-2-yl]acetic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 19-JUN-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   19-JUN-21         0                                  
HETATM    1  N   UNK     0       2.745  -1.916  -0.023  0.00  0.00           N+0
HETATM    2  C   UNK     0       1.723  -1.227   0.365  0.00  0.00           C+0
HETATM    3  N   UNK     0       1.092  -1.533   1.509  0.00  0.00           N+0
HETATM    4  N   UNK     0       1.242  -0.165  -0.337  0.00  0.00           N+0
HETATM    5  C   UNK     0      -0.055   0.478  -0.130  0.00  0.00           C+0
HETATM    6  C   UNK     0      -0.357   1.177  -1.449  0.00  0.00           C+0
HETATM    7  C   UNK     0       1.023   1.567  -1.937  0.00  0.00           C+0
HETATM    8  C   UNK     0       1.870   0.335  -1.581  0.00  0.00           C+0
HETATM    9  C   UNK     0       3.341   0.704  -1.403  0.00  0.00           C+0
HETATM   10  C   UNK     0       4.194  -0.121  -2.327  0.00  0.00           C+0
HETATM   11  O   UNK     0       4.777   0.347  -3.296  0.00  0.00           O+0
HETATM   12  O   UNK     0       4.268  -1.426  -2.000  0.00  0.00           O+0
HETATM   13  H   UNK     0       2.895  -2.658   0.671  0.00  0.00           H+0
HETATM   14  H   UNK     0       1.378  -2.310   2.085  0.00  0.00           H+0
HETATM   15  H   UNK     0       0.401  -0.914   1.902  0.00  0.00           H+0
HETATM   16  H   UNK     0      -0.846  -0.242   0.104  0.00  0.00           H+0
HETATM   17  H   UNK     0       0.022   1.204   0.687  0.00  0.00           H+0
HETATM   18  H   UNK     0      -0.821   0.476  -2.153  0.00  0.00           H+0
HETATM   19  H   UNK     0      -1.025   2.034  -1.326  0.00  0.00           H+0
HETATM   20  H   UNK     0       1.046   1.790  -3.008  0.00  0.00           H+0
HETATM   21  H   UNK     0       1.363   2.458  -1.393  0.00  0.00           H+0
HETATM   22  H   UNK     0       1.726  -0.423  -2.362  0.00  0.00           H+0
HETATM   23  H   UNK     0       3.524   1.753  -1.666  0.00  0.00           H+0
HETATM   24  H   UNK     0       3.710   0.583  -0.379  0.00  0.00           H+0
HETATM   25  H   UNK     0       3.698  -1.652  -1.209  0.00  0.00           H+0
CONECT    1    2   13                                                       
CONECT    2    4    1    3                                                  
CONECT    3    2   14   15                                                  
CONECT    4    2    5    8                                                  
CONECT    5    6    4   16   17                                             
CONECT    6    7    5   18   19                                             
CONECT    7    8    6   20   21                                             
CONECT    8    7    9    4   22                                             
CONECT    9    8   10   23   24                                             
CONECT   10    9   12   11                                                  
CONECT   11   10                                                            
CONECT   12   10   25                                                       
CONECT   13    1                                                            
CONECT   14    3                                                            
CONECT   15    3                                                            
CONECT   16    5                                                            
CONECT   17    5                                                            
CONECT   18    6                                                            
CONECT   19    6                                                            
CONECT   20    7                                                            
CONECT   21    7                                                            
CONECT   22    8                                                            
CONECT   23    9                                                            
CONECT   24    9                                                            
CONECT   25   12                                                            
MASTER        0    0    0    0    0    0    0    0   25    0   50    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₇H₁₃N₃O₂

Average Mass

171.2000 Da

Monoisotopic Mass

171.10078 Da

IUPAC Name

2-[(2S)-1-carbamimidoylpyrrolidin-2-yl]acetic acid

Traditional Name

[(2S)-1-carbamimidoylpyrrolidin-2-yl]acetic acid

CAS Registry Number

Not Available

SMILES

[H]OC(=O)C([H])([H])[C@@]1([H])N(C(=N[H])N([H])[H])C([H])([H])C([H])([H])C1([H])[H]

InChI Identifier

InChI=1S/C7H13N3O2/c8-7(9)10-3-1-2-5(10)4-6(11)12/h5H,1-4H2,(H3,8,9)(H,11,12)/t5-/m0/s1

InChI Key

VYKGYAQKCAHXKR-YFKPBYRVSA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Actaea racemosa	JEOL database	Fabricant, D. S., et al, J. Nat. Prod. 68, 1266 (2005)

Chemical Taxonomy

Classification

Not classified

Physical Properties

State

Not Available

Experimental Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Predicted Properties

Property	Value	Source
logP	-1.1	ALOGPS
logP	-2.2	ChemAxon
logS	-1.8	ALOGPS
pKa (Strongest Acidic)	4.06	ChemAxon
pKa (Strongest Basic)	12.73	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	90.41 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	53.92 m³·mol⁻¹	ChemAxon
Polarizability	17.46 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

129360522

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Fabricant, D. S., et al. (2005). Fabricant, D. S., et al, J. Nat. Prod. 68, 1266 (2005). J. Nat. Prod..

Showing NP-Card for cimipronidine (NP0028440)

MOL for NP0028440 (cimipronidine)

3D MOL for NP0028440 (cimipronidine)

3D SDF for NP0028440 (cimipronidine)

3D-SDF for NP0028440 (cimipronidine)

PDB for NP0028440 (cimipronidine)

3D PDB for NP0028440 (cimipronidine)

SMILES for NP0028440 (cimipronidine)

INCHI for NP0028440 (cimipronidine)

Structure for NP0028440 (cimipronidine)

3D Structure for NP0028440 (cimipronidine)