NP-MRD: Showing NP-Card for cucurbic acid (NP0174482)

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Record Information

Version

1.0

Created at

2022-09-03 11:44:42 UTC

Updated at

2022-09-03 11:44:42 UTC

NP-MRD ID

NP0174482

Secondary Accession Numbers

None

Natural Product Identification

Common Name

cucurbic acid

Description

cucurbic acid is found in Cucurbita pepo.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 35 35  0  0  0  0  0  0  0  0999 V2000
    5.1836    0.6028   -0.5062 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1166   -0.0552    0.3430 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7843    0.6200    0.1768 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7229   -0.0388   -0.2737 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3775    0.6142   -0.4486 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5746   -0.1440    0.4402 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.6484   -1.5847    0.0577 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.2366   -2.3431    1.1553 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1177   -1.9006   -0.1700 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7740   -0.8794    0.7306 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9762    0.3653    0.4075 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.3638    0.9902   -0.8973 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7707    1.4551   -0.8068 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7695    0.7041   -0.9429 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0772    2.8081   -0.5537 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.5935   -0.1004   -1.2815 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8203    1.4988   -1.0210 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.0607    0.8617    0.1428 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0733   -1.1094    0.0446 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4007   -0.0290    1.4057 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6490    1.6642    0.4198 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8597   -1.0845   -0.5172 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1128    0.5425   -1.5134 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4030    1.6697   -0.1498 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1953   -0.0053    1.4898 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0331   -1.8037   -0.8229 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1205   -3.2287    0.9026 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3830   -1.8030   -1.2238 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3020   -2.9352    0.1343 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5078   -1.1598    1.7717 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8470   -0.7822    0.5984 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1547    1.1426    1.1998 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3329    0.2606   -1.7410 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7281    1.8667   -1.0626 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4858    3.3206    0.0638 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  7  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 15  1  0
 13 14  2  0
 11  6  1  0
  1 16  1  0
  1 17  1  0
  1 18  1  0
  2 19  1  0
  2 20  1  0
  3 21  1  0
  4 22  1  0
  5 23  1  0
  5 24  1  0
  6 25  1  1
  7 26  1  6
  8 27  1  0
  9 28  1  0
  9 29  1  0
 10 30  1  0
 10 31  1  0
 11 32  1  1
 12 33  1  0
 12 34  1  0
 15 35  1  0
M  END


  Mrv1652309032213442D          

 15 15  0  0  1  0            999 V2000
    3.4256    1.9393    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7112    2.3518    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9967    1.9393    0.0000 C   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
    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  1  0  0  0  0  0  0  0  0  0
    2.0198    0.8843    0.0000 O   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 C   0  0  2  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
   -1.0558    1.6913    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8405    1.9462    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4427    2.2433    0.0000 O   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
  4  5  1  0  0  0  0
  6  5  1  6  0  0  0
  6  7  1  0  0  0  0
  7  8  1  1  0  0  0
  7  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
  6 11  1  0  0  0  0
 11 12  1  6  0  0  0
 12 13  1  0  0  0  0
 13 14  2  0  0  0  0
 13 15  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0174482

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC\C=C\C[C@@H]1[C@@H](O)CC[C@@H]1CC(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C12H20O3/c1-2-3-4-5-10-9(8-12(14)15)6-7-11(10)13/h3-4,9-11,13H,2,5-8H2,1H3,(H,14,15)/b4-3+/t9-,10+,11+/m1/s1

> <INCHI_KEY>
LYSGIJUGUGJIPS-QDVNPKLESA-N

> <FORMULA>
C12H20O3

> <MOLECULAR_WEIGHT>
212.289

> <EXACT_MASS>
212.141244504

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
35

> <JCHEM_AVERAGE_POLARIZABILITY>
24.28976724781461

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
2-[(1R,2S,3S)-3-hydroxy-2-[(2E)-pent-2-en-1-yl]cyclopentyl]acetic acid

> <ALOGPS_LOGP>
2.86

> <JCHEM_LOGP>
2.028796624

> <ALOGPS_LOGS>
-1.97

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
18.999427344551062

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.849855366098545

> <JCHEM_PKA_STRONGEST_BASIC>
-1.049451099996372

> <JCHEM_POLAR_SURFACE_AREA>
57.53

> <JCHEM_REFRACTIVITY>
59.481700000000004

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.29e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
[(1R,2S,3S)-3-hydroxy-2-[(2E)-pent-2-en-1-yl]cyclopentyl]acetic acid

> <JCHEM_VEBER_RULE>
0

$$$$

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       6.395   3.620   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       5.061   4.390   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       3.727   3.620   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.393   4.390   0.000  0.00  0.00           C+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  O   UNK     0       3.770   1.651   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       1.830  -0.290   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       0.290  -0.290   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -0.186   1.175   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -1.651   1.651   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -1.971   3.157   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0      -3.436   3.633   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0      -0.826   4.188   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7   11                                                  
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10    6   12                                                  
CONECT   12   11   13                                                       
CONECT   13   12   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13                                                            
MASTER        0    0    0    0    0    0    0    0   15    0   30    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₂H₂₀O₃

Average Mass

212.2890 Da

Monoisotopic Mass

212.14124 Da

IUPAC Name

2-[(1R,2S,3S)-3-hydroxy-2-[(2E)-pent-2-en-1-yl]cyclopentyl]acetic acid

Traditional Name

[(1R,2S,3S)-3-hydroxy-2-[(2E)-pent-2-en-1-yl]cyclopentyl]acetic acid

CAS Registry Number

Not Available

SMILES

CC\C=C\C[C@@H]1[C@@H](O)CC[C@@H]1CC(O)=O

InChI Identifier

InChI=1S/C12H20O3/c1-2-3-4-5-10-9(8-12(14)15)6-7-11(10)13/h3-4,9-11,13H,2,5-8H2,1H3,(H,14,15)/b4-3+/t9-,10+,11+/m1/s1

InChI Key

LYSGIJUGUGJIPS-QDVNPKLESA-N

Experimental Spectra

Not Available

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 25 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Cucurbita pepo	LOTUS Database	35616633

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	2.86	ALOGPS
logP	2.03	ChemAxon
logS	-2	ALOGPS
pKa (Strongest Acidic)	4.85	ChemAxon
pKa (Strongest Basic)	-1	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	57.53 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	59.48 m³·mol⁻¹	ChemAxon
Polarizability	24.29 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for cucurbic acid (NP0174482)

MOL for NP0174482 (cucurbic acid)

3D MOL for NP0174482 (cucurbic acid)

3D SDF for NP0174482 (cucurbic acid)

3D-SDF for NP0174482 (cucurbic acid)

PDB for NP0174482 (cucurbic acid)

3D PDB for NP0174482 (cucurbic acid)

SMILES for NP0174482 (cucurbic acid)

INCHI for NP0174482 (cucurbic acid)

Structure for NP0174482 (cucurbic acid)

3D Structure for NP0174482 (cucurbic acid)