NP-MRD: Showing NP-Card for Phaeophorbide a (NP0081875)

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Record Information

Version

2.0

Created at

2022-04-29 02:56:27 UTC

Updated at

2022-04-29 02:56:27 UTC

NP-MRD ID

NP0081875

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Phaeophorbide a

Description

Phaeophorbide a is found in Clerodendrum calamitosum, Isatis tinctoria and Saussurea medusa.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652305301923492D          

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M  END

     RDKit          3D

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M  END


  Mrv1652305301923492D          

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    3.4470    1.0892    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6751    2.8404    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0006   -2.0887    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4615   -2.0469    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2480   -2.8856    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6606   -3.6000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2141   -2.8856    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.0232   -3.6000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1983   -3.6000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2141   -4.3144    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0391   -4.3144    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4393   -2.0469    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.4393   -2.8718    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1537   -3.2844    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1537   -4.1094    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4393   -4.5218    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8682   -4.5218    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0236   -1.4625    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.8205   -1.6760    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1 24  1  0  0  0  0
 15  1  2  0  0  0  0
  1 11  1  0  0  0  0
  2  3  1  0  0  0  0
 24  2  1  0  0  0  0
 20  2  2  0  0  0  0
  3  4  2  0  0  0  0
  4 12  1  0  0  0  0
 17  4  1  0  0  0  0
  5  6  1  0  0  0  0
 12  5  2  0  0  0  0
 23  5  1  0  0  0  0
  6  7  2  0  0  0  0
  7 13  1  0  0  0  0
  7 18  1  0  0  0  0
  8 28  2  0  0  0  0
 29  8  1  0  0  0  0
 13  8  1  0  0  0  0
  9 28  1  0  0  0  0
 14  9  2  0  0  0  0
 37  9  1  0  0  0  0
 10 11  2  0  0  0  0
 14 10  1  0  0  0  0
 43 10  1  0  0  0  0
 20 15  1  0  0  0  0
 15 16  1  0  0  0  0
 17 23  2  0  0  0  0
 17 27  1  0  0  0  0
 18 29  2  0  0  0  0
 18 19  1  0  0  0  0
 43 37  1  0  0  0  0
 20 21  1  0  0  0  0
 21 22  2  0  0  0  0
 23 25  1  0  0  0  0
 25 26  1  0  0  0  0
 28 32  1  0  0  0  0
 29 30  1  0  0  0  0
 32 30  1  0  0  0  0
 30 31  2  0  0  0  0
 32 34  1  6  0  0  0
 34 33  2  0  0  0  0
 34 35  1  0  0  0  0
 35 36  1  0  0  0  0
 39 38  1  0  0  0  0
 37 38  1  1  0  0  0
 39 40  1  0  0  0  0
 40 42  1  0  0  0  0
 40 41  2  0  0  0  0
 43 44  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0081875

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CCC1=C(C)\C2=C\C3=C(C=C)C(C)=C(N3)\C=C3/N=C([C@@H](CCC(O)=O)[C@@H]3C)C3=C4N\C(=C/C1=N2)C(C)=C4C(=O)[C@@H]3C(=O)OC

> <INCHI_IDENTIFIER>
InChI=1S/C35H36N4O5/c1-8-19-15(3)22-12-24-17(5)21(10-11-28(40)41)32(38-24)30-31(35(43)44-7)34(42)29-18(6)25(39-33(29)30)14-27-20(9-2)16(4)23(37-27)13-26(19)36-22/h8,12-14,17,21,31,36,39H,1,9-11H2,2-7H3,(H,40,41)/b22-12-,23-13-,24-12-,25-14-,26-13-,27-14-,32-30-/t17-,21-,31+/m0/s1

> <INCHI_KEY>
NSFSLUUZQIAOOX-QEWKCGBTSA-N

> <FORMULA>
C35H36N4O5

> <MOLECULAR_WEIGHT>
592.696

> <EXACT_MASS>
592.268570275

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
80

> <JCHEM_AVERAGE_POLARIZABILITY>
67.63964991545411

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3-[(3R,21S,22S)-16-ethenyl-11-ethyl-3-(methoxycarbonyl)-12,17,21,26-tetramethyl-4-oxo-7,23,24,25-tetraazahexacyclo[18.2.1.1^{5,8}.1^{10,13}.1^{15,18}.0^{2,6}]hexacosa-1(23),2(6),5(26),8,10(25),11,13,15,17,19-decaen-22-yl]propanoic acid

> <ALOGPS_LOGP>
4.53

> <JCHEM_LOGP>
4.519428973464704

> <ALOGPS_LOGS>
-4.56

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
6

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
3.7441587530268623

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.7650024120395367

> <JCHEM_PKA_STRONGEST_BASIC>
6.777127027458991

> <JCHEM_POLAR_SURFACE_AREA>
138.03

> <JCHEM_REFRACTIVITY>
167.465

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.63e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-[(3R,21S,22S)-16-ethenyl-11-ethyl-3-(methoxycarbonyl)-12,17,21,26-tetramethyl-4-oxo-7,23,24,25-tetraazahexacyclo[18.2.1.1^{5,8}.1^{10,13}.1^{15,18}.0^{2,6}]hexacosa-1(23),2(6),5(26),8,10(25),11,13,15,17,19-decaen-22-yl]propanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 30-MAY-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   30-MAY-19         0                                  
HETATM    1  C   UNK     0      -3.076   1.321   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -1.323   3.113   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.001   3.892   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.365   3.113   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       3.118   1.321   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       3.897  -0.003   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       3.118  -1.328   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       1.365  -3.120   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -1.323  -3.120   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -3.076  -1.328   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -3.855  -0.003   0.000  0.00  0.00           C+0
HETATM   12  N   UNK     0       1.598   1.594   0.000  0.00  0.00           N+0
HETATM   13  N   UNK     0       1.598  -1.600   0.000  0.00  0.00           N+0
HETATM   14  N   UNK     0      -1.557  -1.600   0.000  0.00  0.00           N+0
HETATM   15  C   UNK     0      -3.777   2.724   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      -5.265   3.122   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       2.728   3.814   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       3.858  -2.730   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       5.345  -3.129   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      -2.687   3.814   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      -3.085   5.302   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      -4.573   5.701   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       3.858   2.724   0.000  0.00  0.00           C+0
HETATM   24  N   UNK     0      -1.557   1.594   0.000  0.00  0.00           N+0
HETATM   25  C   UNK     0       5.345   3.122   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       6.434   2.033   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       3.127   5.302   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       0.001  -3.899   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       2.728  -3.821   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       2.330  -5.386   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0       3.100  -6.720   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0       0.400  -5.386   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0      -1.910  -6.720   0.000  0.00  0.00           O+0
HETATM   34  C   UNK     0      -0.370  -6.720   0.000  0.00  0.00           C+0
HETATM   35  O   UNK     0       0.400  -8.054   0.000  0.00  0.00           O+0
HETATM   36  C   UNK     0       1.940  -8.054   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0      -2.687  -3.821   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0      -2.687  -5.361   0.000  0.00  0.00           C+0
HETATM   39  C   UNK     0      -4.020  -6.131   0.000  0.00  0.00           C+0
HETATM   40  C   UNK     0      -4.020  -7.671   0.000  0.00  0.00           C+0
HETATM   41  O   UNK     0      -2.687  -8.441   0.000  0.00  0.00           O+0
HETATM   42  O   UNK     0      -5.354  -8.441   0.000  0.00  0.00           O+0
HETATM   43  C   UNK     0      -3.777  -2.730   0.000  0.00  0.00           C+0
HETATM   44  C   UNK     0      -5.265  -3.129   0.000  0.00  0.00           C+0
CONECT    1   24   15   11                                                  
CONECT    2    3   24   20                                                  
CONECT    3    2    4                                                       
CONECT    4    3   12   17                                                  
CONECT    5    6   12   23                                                  
CONECT    6    5    7                                                       
CONECT    7    6   13   18                                                  
CONECT    8   28   29   13                                                  
CONECT    9   28   14   37                                                  
CONECT   10   11   14   43                                                  
CONECT   11    1   10                                                       
CONECT   12    4    5                                                       
CONECT   13    7    8                                                       
CONECT   14    9   10                                                       
CONECT   15    1   20   16                                                  
CONECT   16   15                                                            
CONECT   17    4   23   27                                                  
CONECT   18    7   29   19                                                  
CONECT   19   18                                                            
CONECT   20    2   15   21                                                  
CONECT   21   20   22                                                       
CONECT   22   21                                                            
CONECT   23    5   17   25                                                  
CONECT   24    1    2                                                       
CONECT   25   23   26                                                       
CONECT   26   25                                                            
CONECT   27   17                                                            
CONECT   28    8    9   32                                                  
CONECT   29    8   18   30                                                  
CONECT   30   29   32   31                                                  
CONECT   31   30                                                            
CONECT   32   28   30   34                                                  
CONECT   33   34                                                            
CONECT   34   32   33   35                                                  
CONECT   35   34   36                                                       
CONECT   36   35                                                            
CONECT   37    9   43   38                                                  
CONECT   38   39   37                                                       
CONECT   39   38   40                                                       
CONECT   40   39   42   41                                                  
CONECT   41   40                                                            
CONECT   42   40                                                            
CONECT   43   10   37   44                                                  
CONECT   44   43                                                            
MASTER        0    0    0    0    0    0    0    0   44    0   98    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₃₅H₃₆N₄O₅

Average Mass

592.6960 Da

Monoisotopic Mass

592.26857 Da

IUPAC Name

3-[(3R,21S,22S)-16-ethenyl-11-ethyl-3-(methoxycarbonyl)-12,17,21,26-tetramethyl-4-oxo-7,23,24,25-tetraazahexacyclo[18.2.1.1^{5,8}.1^{10,13}.1^{15,18}.0^{2,6}]hexacosa-1(23),2(6),5(26),8,10(25),11,13,15,17,19-decaen-22-yl]propanoic acid

Traditional Name

CAS Registry Number

Not Available

SMILES

CCC1=C(C)\C2=C\C3=C(C=C)C(C)=C(N3)\C=C3/N=C([C@@H](CCC(O)=O)[C@@H]3C)C3=C4N\C(=C/C1=N2)C(C)=C4C(=O)[C@@H]3C(=O)OC

InChI Identifier

InChI=1S/C35H36N4O5/c1-8-19-15(3)22-12-24-17(5)21(10-11-28(40)41)32(38-24)30-31(35(43)44-7)34(42)29-18(6)25(39-33(29)30)14-27-20(9-2)16(4)23(37-27)13-26(19)36-22/h8,12-14,17,21,31,36,39H,1,9-11H2,2-7H3,(H,40,41)/b22-12-,23-13-,24-12-,25-14-,26-13-,27-14-,32-30-/t17-,21-,31+/m0/s1

InChI Key

NSFSLUUZQIAOOX-QEWKCGBTSA-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, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, 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
Clerodendrum calamitosum	LOTUS Database	35616633
Isatis tinctoria	Plant	KNApSAcK
Saussurea medusa	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	4.53	ALOGPS
logP	4.52	ChemAxon
logS	-4.6	ALOGPS
pKa (Strongest Acidic)	2.77	ChemAxon
pKa (Strongest Basic)	6.78	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	138.03 Å²	ChemAxon
Rotatable Bond Count	7	ChemAxon
Refractivity	167.46 m³·mol⁻¹	ChemAxon
Polarizability	67.64 Å³	ChemAxon
Number of Rings	6	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	ChemAxon

External Links

Not Available

References

General References

Not Available

Showing NP-Card for Phaeophorbide a (NP0081875)

MOL for NP0081875 (Phaeophorbide a)

3D MOL for NP0081875 (Phaeophorbide a)

3D SDF for NP0081875 (Phaeophorbide a)

3D-SDF for NP0081875 (Phaeophorbide a)

PDB for NP0081875 (Phaeophorbide a)

3D PDB for NP0081875 (Phaeophorbide a)

SMILES for NP0081875 (Phaeophorbide a)

INCHI for NP0081875 (Phaeophorbide a)

Structure for NP0081875 (Phaeophorbide a)

3D Structure for NP0081875 (Phaeophorbide a)