NP-MRD: Showing NP-Card for Protochlorophyll a (NP0049326)

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Record Information

Version

2.0

Created at

2022-03-17 21:10:41 UTC

Updated at

2022-03-17 21:10:41 UTC

NP-MRD ID

NP0049326

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Protochlorophyll a

Description

Protochlorophyll a was first documented in 2008 (PMID: 18396166). Based on a literature review a significant number of articles have been published on Protochlorophyll a (PMID: 32757305) (PMID: 29569330) (PMID: 27810676) (PMID: 22827616) (PMID: 18221490).

Structure

MOL SDF PDB SMILES InChI


  Mrv1652303172222102D          

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M  RAD  2  20   2  26   2
M  END


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M  RAD  2  20   2  26   2
M  END
> <DATABASE_ID>
NP0049326

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC(=O)C1C(=O)C2=C3N4C(C=C5C(C=C)=C(C)C6=[N]5[Mg]44N5C(=CC7=[N]4C(C(CCC(=O)OC\C=C(\C)CCCC(C)CCCC(C)CCCC(C)C)=C7C)=C13)C(C)=C(C=C)C5=C6)=C2C

> <INCHI_IDENTIFIER>
InChI=1S/C55H68N4O5.Mg/c1-13-39-35(8)42-28-44-37(10)41(24-25-48(60)64-27-26-34(7)23-17-22-33(6)21-16-20-32(5)19-15-18-31(3)4)52(58-44)50-51(55(62)63-12)54(61)49-38(11)45(59-53(49)50)30-47-40(14-2)36(9)43(57-47)29-46(39)56-42;/h13-14,26,28-33,51H,1-2,15-25,27H2,3-12H3;/q-2;+2/b34-26-,42-28-,45-30-,46-29-;

> <INCHI_KEY>
KVVZXIKFBROVBL-ZVDHPXDYSA-N

> <FORMULA>
C55H68MgN4O5

> <MOLECULAR_WEIGHT>
889.477

> <EXACT_MASS>
888.50401301

> <JCHEM_ACCEPTOR_COUNT>
0

> <JCHEM_ATOM_COUNT>
133

> <JCHEM_AVERAGE_POLARIZABILITY>
109.91365675308693

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <ALOGPS_LOGP>
2.60

> <ALOGPS_LOGS>
-6.58

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
9

> <JCHEM_POLAR_SURFACE_AREA>
116.26

> <JCHEM_REFRACTIVITY>
272.3903000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
22

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
2.36e-04 g/l

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 17-MAR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   17-MAR-22         0                                  
HETATM    1  C   UNK     0      -6.592  -3.667   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0      -5.804  -2.343   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0      -4.264  -2.363   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0      -3.512  -3.707   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0      -3.477  -1.040   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -4.085   0.375   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      -5.587   0.715   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0      -2.927   1.391   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -1.604   0.603   0.000  0.00  0.00           C+0
HETATM   10  N   UNK     0      -0.446   1.619   0.000  0.00  0.00           N+0
HETATM   11  C   UNK     0      -1.054   3.034   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       0.327   4.200   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       1.845   4.461   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       2.875   5.606   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       2.555   7.112   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       3.699   8.142   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       4.282   4.979   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       5.616   5.749   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       4.121   3.448   0.000  0.00  0.00           C+0
HETATM   20  N   UNK     0       2.615   3.127   0.000  0.00  0.00           N+0
HETATM   21 Mg   UNK     0       1.848   0.573   0.000  0.00  0.00          Mg+0
HETATM   22  N   UNK     0       4.353  -0.358   0.000  0.00  0.00           N+0
HETATM   23  C   UNK     0       4.673  -1.864   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       3.156  -3.169   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       1.638  -3.430   0.000  0.00  0.00           C+0
HETATM   26  N   UNK     0       0.868  -2.096   0.000  0.00  0.00           N+0
HETATM   27  C   UNK     0      -0.638  -2.416   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      -0.799  -3.948   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      -2.133  -4.718   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      -2.133  -6.258   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      -0.799  -7.028   0.000  0.00  0.00           C+0
HETATM   32  O   UNK     0       0.534  -6.258   0.000  0.00  0.00           O+0
HETATM   33  O   UNK     0      -0.799  -8.568   0.000  0.00  0.00           O+0
HETATM   34  C   UNK     0       0.534  -9.338   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0       0.534 -10.878   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0       1.868 -11.648   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0       1.868 -13.188   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0       3.202 -10.878   0.000  0.00  0.00           C+0
HETATM   39  C   UNK     0       4.535 -11.648   0.000  0.00  0.00           C+0
HETATM   40  C   UNK     0       5.869 -10.878   0.000  0.00  0.00           C+0
HETATM   41  C   UNK     0       7.203 -11.648   0.000  0.00  0.00           C+0
HETATM   42  C   UNK     0       7.203 -13.188   0.000  0.00  0.00           C+0
HETATM   43  C   UNK     0       8.536 -10.878   0.000  0.00  0.00           C+0
HETATM   44  C   UNK     0       9.870 -11.648   0.000  0.00  0.00           C+0
HETATM   45  C   UNK     0      11.204 -10.878   0.000  0.00  0.00           C+0
HETATM   46  C   UNK     0      12.537 -11.648   0.000  0.00  0.00           C+0
HETATM   47  C   UNK     0      12.537 -13.188   0.000  0.00  0.00           C+0
HETATM   48  C   UNK     0      13.871 -10.878   0.000  0.00  0.00           C+0
HETATM   49  C   UNK     0      15.205 -11.648   0.000  0.00  0.00           C+0
HETATM   50  C   UNK     0      16.538 -10.878   0.000  0.00  0.00           C+0
HETATM   51  C   UNK     0      17.872 -11.648   0.000  0.00  0.00           C+0
HETATM   52  C   UNK     0      19.206 -10.878   0.000  0.00  0.00           C+0
HETATM   53  C   UNK     0      17.872 -13.188   0.000  0.00  0.00           C+0
HETATM   54  C   UNK     0       0.608  -4.574   0.000  0.00  0.00           C+0
HETATM   55  C   UNK     0       1.378  -5.908   0.000  0.00  0.00           C+0
HETATM   56  C   UNK     0      -1.943  -0.899   0.000  0.00  0.00           C+0
HETATM   57  C   UNK     0       6.205  -2.025   0.000  0.00  0.00           C+0
HETATM   58  C   UNK     0       6.975  -3.359   0.000  0.00  0.00           C+0
HETATM   59  C   UNK     0       6.831  -0.618   0.000  0.00  0.00           C+0
HETATM   60  C   UNK     0       8.338  -0.298   0.000  0.00  0.00           C+0
HETATM   61  C   UNK     0       9.368  -1.442   0.000  0.00  0.00           C+0
HETATM   62  C   UNK     0       5.687   0.412   0.000  0.00  0.00           C+0
HETATM   63  C   UNK     0       5.426   1.930   0.000  0.00  0.00           C+0
HETATM   64  C   UNK     0      -2.587   2.893   0.000  0.00  0.00           C+0
HETATM   65  C   UNK     0      -3.603   4.050   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6   56                                                  
CONECT    6    5    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    9   64                                                  
CONECT    9    8   10   56                                                  
CONECT   10    9   11   21                                                  
CONECT   11   10   12   64                                                  
CONECT   12   11   13                                                       
CONECT   13   12   14   20                                                  
CONECT   14   13   15   17                                                  
CONECT   15   14   16                                                       
CONECT   16   15                                                            
CONECT   17   14   18   19                                                  
CONECT   18   17                                                            
CONECT   19   17   20   63                                                  
CONECT   20   19   13   21                                                  
CONECT   21   20   10   22   26                                             
CONECT   22   21   23   62                                                  
CONECT   23   22   24   57                                                  
CONECT   24   23   25                                                       
CONECT   25   24   26   54                                                  
CONECT   26   25   21   27                                                  
CONECT   27   26   28   56                                                  
CONECT   28   27   29   54                                                  
CONECT   29   28   30                                                       
CONECT   30   29   31                                                       
CONECT   31   30   32   33                                                  
CONECT   32   31                                                            
CONECT   33   31   34                                                       
CONECT   34   33   35                                                       
CONECT   35   34   36                                                       
CONECT   36   35   37   38                                                  
CONECT   37   36                                                            
CONECT   38   36   39                                                       
CONECT   39   38   40                                                       
CONECT   40   39   41                                                       
CONECT   41   40   42   43                                                  
CONECT   42   41                                                            
CONECT   43   41   44                                                       
CONECT   44   43   45                                                       
CONECT   45   44   46                                                       
CONECT   46   45   47   48                                                  
CONECT   47   46                                                            
CONECT   48   46   49                                                       
CONECT   49   48   50                                                       
CONECT   50   49   51                                                       
CONECT   51   50   52   53                                                  
CONECT   52   51                                                            
CONECT   53   51                                                            
CONECT   54   28   25   55                                                  
CONECT   55   54                                                            
CONECT   56   27    5    9                                                  
CONECT   57   23   58   59                                                  
CONECT   58   57                                                            
CONECT   59   57   60   62                                                  
CONECT   60   59   61                                                       
CONECT   61   60                                                            
CONECT   62   59   22   63                                                  
CONECT   63   62   19                                                       
CONECT   64   11    8   65                                                  
CONECT   65   64                                                            
MASTER        0    0    0    0    0    0    0    0   65    0  146    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₅₅H₆₈MgN₄O₅

Average Mass

889.4770 Da

Monoisotopic Mass

888.50401 Da

IUPAC Name

Not Available

Traditional Name

Not Available

CAS Registry Number

18433-30-2

SMILES

COC(=O)C1C(=O)C2=C3N4C(C=C5C(C=C)=C(C)C6=[N]5[Mg]44N5C(=CC7=[N]4C(C(CCC(=O)OC\C=C(\C)CCCC(C)CCCC(C)CCCC(C)C)=C7C)=C13)C(C)=C(C=C)C5=C6)=C2C

InChI Identifier

InChI=1S/C55H68N4O5.Mg/c1-13-39-35(8)42-28-44-37(10)41(24-25-48(60)64-27-26-34(7)23-17-22-33(6)21-16-20-32(5)19-15-18-31(3)4)52(58-44)50-51(55(62)63-12)54(61)49-38(11)45(59-53(49)50)30-47-40(14-2)36(9)43(57-47)29-46(39)56-42;/h13-14,26,28-33,51H,1-2,15-25,27H2,3-12H3;/q-2;+2/b34-26-,42-28-,45-30-,46-29-;

InChI Key

KVVZXIKFBROVBL-ZVDHPXDYSA-N

Experimental Spectra

Not Available

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Hordeum vulgare	FooDB	Dr. Duke's Phytochemical and Ethnobotanical Databases

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	2.6	ALOGPS
logS	-6.6	ALOGPS
Hydrogen Acceptor Count	0	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	116.26 Å²	ChemAxon
Rotatable Bond Count	22	ChemAxon
Refractivity	272.39 m³·mol⁻¹	ChemAxon
Polarizability	109.91 Å³	ChemAxon
Number of Rings	9	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	ChemAxon

External Links

HMDB ID

HMDB0303697

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

Not Available

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Taniguchi M, Lindsey JS: Absorption and Fluorescence Spectral Database of Chlorophylls and Analogues. Photochem Photobiol. 2021 Jan;97(1):136-165. doi: 10.1111/php.13319. Epub 2020 Nov 11. [PubMed:32757305 ]
Saga Y, Miyagi K: Characterization of 3-Acetyl Chlorophyll a and 3-Acetyl Protochlorophyll a Accommodated in the B800 Binding Sites of Photosynthetic Light-Harvesting Complex 2 in the Purple Photosynthetic Bacterium Rhodoblastus acidophilus. Photochem Photobiol. 2018 Jul;94(4):698-704. doi: 10.1111/php.12919. Epub 2018 Apr 26. [PubMed:29569330 ]
Matsuda K, Shimoda Y, Tanaka A, Ito H: Chlorophyll a is a favorable substrate for Chlamydomonas Mg-dechelatase encoded by STAY-GREEN. Plant Physiol Biochem. 2016 Dec;109:365-373. doi: 10.1016/j.plaphy.2016.10.020. Epub 2016 Oct 24. [PubMed:27810676 ]
Saga Y, Hirai Y, Sadaoka K, Isaji M, Tamiaki H: Structure-dependent demetalation kinetics of chlorophyll a analogs under acidic conditions. Photochem Photobiol. 2013 Jan-Feb;89(1):68-73. doi: 10.1111/j.1751-1097.2012.01213.x. Epub 2012 Aug 30. [PubMed:22827616 ]
Reisinger V, Ploscher M, Eichacker LA: Lil3 assembles as chlorophyll-binding protein complex during deetiolation. FEBS Lett. 2008 Apr 30;582(10):1547-51. doi: 10.1016/j.febslet.2008.03.042. Epub 2008 Apr 7. [PubMed:18396166 ]
Reisinger V, Hertle AP, Ploscher M, Eichacker LA: Cytochrome b6f is a dimeric protochlorophyll a binding complex in etioplasts. FEBS J. 2008 Mar;275(5):1018-24. doi: 10.1111/j.1742-4658.2008.06268.x. Epub 2008 Jan 25. [PubMed:18221490 ]

Showing NP-Card for Protochlorophyll a (NP0049326)

MOL for NP0049326 (Protochlorophyll a)

3D MOL for NP0049326 (Protochlorophyll a)

3D SDF for NP0049326 (Protochlorophyll a)

3D-SDF for NP0049326 (Protochlorophyll a)

PDB for NP0049326 (Protochlorophyll a)

3D PDB for NP0049326 (Protochlorophyll a)

SMILES for NP0049326 (Protochlorophyll a)

INCHI for NP0049326 (Protochlorophyll a)

Structure for NP0049326 (Protochlorophyll a)

3D Structure for NP0049326 (Protochlorophyll a)