NP-MRD: Showing NP-Card for porphyrin (NP0152672)

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Record Information

Version

2.0

Created at

2022-09-02 09:12:03 UTC

Updated at

2022-09-02 09:12:03 UTC

NP-MRD ID

NP0152672

Secondary Accession Numbers

None

Natural Product Identification

Common Name

porphyrin

Description

Porphyrin is also known as 21H,23H-porphin. porphyrin is found in Arabidopsis thaliana and Salmonella enterica. Porphyrin is a very strong basic compound (based on its pKa).

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 38 42  0  0  0  0  0  0  0  0999 V2000
   -3.4513   -2.8751    0.4733 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4760   -3.7533    0.2990 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2570   -2.9993    0.1002 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0595   -3.3863   -0.1192 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1592   -2.5221   -0.3187 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0679   -2.8314   -1.3529 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9959   -1.8286   -1.3475 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6180   -0.9496   -0.3134 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3974    0.2148   -0.1112 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9140    1.4907    0.1189 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5697    1.6942    0.1695 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.2931    2.9937    0.4108 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0494    3.3714    0.5003 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1605    2.5311    0.3523 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2411    2.9890   -0.4382 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1742    1.9935   -0.4476 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6268    0.9541    0.3437 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3787   -0.2258    0.4941 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8956   -1.5360    0.3929 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5788   -1.6927    0.1679 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4204    1.3004    0.8143 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.5759    3.6429    0.5169 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5723    2.7542    0.3439 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5080   -1.3834    0.3019 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5071   -3.0645    0.6503 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6040   -4.8258    0.3096 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2256   -4.4822   -0.1504 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0685   -3.6959   -2.0405 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8625   -1.7601   -2.0321 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4977    0.1457   -0.1481 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1835    4.4524    0.6895 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3490    3.9613   -0.9579 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1500    2.0188   -0.9659 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4670   -0.1701    0.6938 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7659    0.6898    1.4860 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7317    4.6933    0.7079 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6246    3.0013    0.3786 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9948   -0.9104    1.1721 H   0  0  0  0  0  0  0  0  0  0  0  0
 21 14  1  0
 14 15  2  0
 15 16  1  0
 16 17  2  0
 17 18  1  0
 18 19  2  0
 19  1  1  0
  1  2  2  0
  2  3  1  0
  3  4  1  0
  4  5  2  0
  5 24  1  0
 24  8  1  0
  8  7  1  0
  7  6  2  0
  8  9  2  0
  9 10  1  0
 10 11  2  0
 11 12  1  0
 12 22  1  0
 22 23  2  0
 12 13  2  0
  3 20  2  0
 17 21  1  0
 20 19  1  0
 13 14  1  0
  6  5  1  0
 23 10  1  0
 21 35  1  0
 15 32  1  0
 16 33  1  0
 18 34  1  0
  1 25  1  0
  2 26  1  0
  4 27  1  0
 24 38  1  0
  7 29  1  0
  6 28  1  0
  9 30  1  0
 22 36  1  0
 23 37  1  0
 13 31  1  0
M  END


  Mrv1533004241512572D          

 24 28  0  0  0  0            999 V2000
   -2.0430   -1.5110    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4819   -2.0624    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7243   -1.6459    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0112   -2.0494    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7106   -1.6627    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5044   -2.0364    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0558   -1.4752    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6683   -0.6881    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0427    0.0179    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6265    0.7462    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0297    1.5110    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4686    2.0624    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7107    1.6752    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0047    2.0496    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7239    1.6627    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4588    2.0076    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0393    1.4169    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6818    0.7174    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0558   -0.0472    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6690   -0.7465    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8480   -0.8857    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8926    0.8706    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.8643    0.8567    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.8501   -0.8709    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  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
  5  6  2  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
 10 11  1  0  0  0  0
 11 12  2  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  2  0  0  0  0
 15 16  1  0  0  0  0
 16 17  2  0  0  0  0
 17 18  1  0  0  0  0
 18 19  2  0  0  0  0
 19 20  1  0  0  0  0
  1 20  1  0  0  0  0
 20 21  2  0  0  0  0
  3 21  1  0  0  0  0
 18 22  1  0  0  0  0
 15 22  1  0  0  0  0
 13 23  2  0  0  0  0
 10 23  1  0  0  0  0
  8 24  1  0  0  0  0
  5 24  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0152672

> <DATABASE_NAME>
NP-MRD

> <SMILES>
N1C2=CC=C1\C=C1\C=CC(\C=C3/N\C(\C=C3)=C/C3=N/C(/C=C3)=C\2)=N1

> <INCHI_IDENTIFIER>
InChI=1S/C20H14N4/c1-2-14-10-16-5-6-18(23-16)12-20-8-7-19(24-20)11-17-4-3-15(22-17)9-13(1)21-14/h1-12,21,24H/b13-9-,14-10-,15-9-,16-10-,17-11-,18-12-,19-11-,20-12-

> <INCHI_KEY>
RKCAIXNGYQCCAL-CEVVSZFKSA-N

> <FORMULA>
C20H14N4

> <MOLECULAR_WEIGHT>
310.36

> <EXACT_MASS>
310.121846467

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
38

> <JCHEM_AVERAGE_POLARIZABILITY>
34.71562867779166

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
21,22,23,24-tetraazapentacyclo[16.2.1.1³,⁶.1⁸,¹¹.1¹³,¹⁶]tetracosa-1,3,5,7,9,11(23),12,14,16,18(21),19-undecaene

> <ALOGPS_LOGP>
3.04

> <JCHEM_LOGP>
4.632079222

> <ALOGPS_LOGS>
-3.85

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
15.268390849976726

> <JCHEM_PKA_STRONGEST_ACIDIC>
14.666268640916226

> <JCHEM_PKA_STRONGEST_BASIC>
5.228923767658881

> <JCHEM_POLAR_SURFACE_AREA>
57.36

> <JCHEM_REFRACTIVITY>
92.45660000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.36e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
porphyrin

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 24-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-APR-15         0                                  
HETATM    1  C   UNK     0      -3.814  -2.821   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -2.766  -3.850   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -1.352  -3.072   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.021  -3.826   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.326  -3.104   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.808  -3.801   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       3.837  -2.754   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       3.114  -1.284   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       3.813   0.033   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       3.036   1.393   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       3.789   2.821   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       2.741   3.850   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       1.327   3.127   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       0.009   3.826   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -1.351   3.104   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      -2.723   3.748   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      -3.807   2.645   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      -3.139   1.339   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      -3.837  -0.088   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      -3.115  -1.393   0.000  0.00  0.00           C+0
HETATM   21  N   UNK     0      -1.583  -1.653   0.000  0.00  0.00           N+0
HETATM   22  N   UNK     0      -1.666   1.625   0.000  0.00  0.00           N+0
HETATM   23  N   UNK     0       1.613   1.599   0.000  0.00  0.00           N+0
HETATM   24  N   UNK     0       1.587  -1.626   0.000  0.00  0.00           N+0
CONECT    1    2   20                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4   21                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6   24                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9   24                                                  
CONECT    9    8   10                                                       
CONECT   10    9   11   23                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14   23                                                  
CONECT   14   13   15                                                       
CONECT   15   14   16   22                                                  
CONECT   16   15   17                                                       
CONECT   17   16   18                                                       
CONECT   18   17   19   22                                                  
CONECT   19   18   20                                                       
CONECT   20   19    1   21                                                  
CONECT   21   20    3                                                       
CONECT   22   18   15                                                       
CONECT   23   13   10                                                       
CONECT   24    8    5                                                       
MASTER        0    0    0    0    0    0    0    0   24    0   56    0
END

View in JSmol

Synonyms

Value	Source
21H,23H-Porphin	ChEBI
21H,23H-Porphine	ChEBI
Porphine	ChEBI

Chemical Formula

C₂₀H₁₄N₄

Average Mass

310.3600 Da

Monoisotopic Mass

310.12185 Da

IUPAC Name

21,22,23,24-tetraazapentacyclo[16.2.1.1³,⁶.1⁸,¹¹.1¹³,¹⁶]tetracosa-1,3,5,7,9,11(23),12,14,16,18(21),19-undecaene

Traditional Name

porphyrin

CAS Registry Number

Not Available

SMILES

N1C2=CC=C1\C=C1\C=CC(\C=C3/N\C(\C=C3)=C/C3=N/C(/C=C3)=C\2)=N1

InChI Identifier

InChI=1S/C20H14N4/c1-2-14-10-16-5-6-18(23-16)12-20-8-7-19(24-20)11-17-4-3-15(22-17)9-13(1)21-14/h1-12,21,24H/b13-9-,14-10-,15-9-,16-10-,17-11-,18-12-,19-11-,20-12-

InChI Key

RKCAIXNGYQCCAL-CEVVSZFKSA-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
Arabidopsis thaliana	LOTUS Database	35616633
Salmonella enterica	LOTUS Database	35616633

Chemical Taxonomy

Description

This compound belongs to the class of organic compounds known as porphyrins. These are compounds containing a fundamental skeleton of four pyrrole nuclei united through the alpha-positions by four methine groups to form a macrocyclic structure.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Tetrapyrroles and derivatives

Sub Class

Porphyrins

Direct Parent

Porphyrins

Alternative Parents

Substituents

Porphyrin
Heteroaromatic compound
Pyrrole
Azacycle
Organic nitrogen compound
Organopnictogen compound
Hydrocarbon derivative
Organonitrogen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

Not Available

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	3.04	ALOGPS
logP	4.63	ChemAxon
logS	-3.8	ALOGPS
pKa (Strongest Acidic)	14.67	ChemAxon
pKa (Strongest Basic)	5.23	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	2	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	57.36 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	92.46 m³·mol⁻¹	ChemAxon
Polarizability	34.72 Å³	ChemAxon
Number of Rings	5	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

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

C05113

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Porphyrin

METLIN ID

Not Available

PubChem Compound

Not Available

PDB ID

Not Available

ChEBI ID

8337

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for porphyrin (NP0152672)

MOL for NP0152672 (porphyrin)

3D MOL for NP0152672 (porphyrin)

3D SDF for NP0152672 (porphyrin)

3D-SDF for NP0152672 (porphyrin)

PDB for NP0152672 (porphyrin)

3D PDB for NP0152672 (porphyrin)

SMILES for NP0152672 (porphyrin)

INCHI for NP0152672 (porphyrin)

Structure for NP0152672 (porphyrin)

3D Structure for NP0152672 (porphyrin)