NP-MRD: Showing NP-Card for Chlorophyll d (NP0337295)

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Record Information

Version

2.0

Created at

2024-09-11 10:12:40 UTC

Updated at

2024-09-11 10:12:40 UTC

NP-MRD ID

NP0337295

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Chlorophyll d

Description

Chlorophyll d belongs to the class of organic compounds known as chlorins. These are large heterocyclic aromatic ring systems consisting, at the core, of three pyrroles and one pyrroline coupled through four methine linkages. Chlorophyll d was first documented in 2024 (PMID: 39038640). Based on a literature review a small amount of articles have been published on Chlorophyll d (PMID: 38851184) (PMID: 38394197) (PMID: 38286009) (PMID: 37772760).

Structure

MOL SDF PDB SMILES InChI


  Mrv2104 05262312442D          

 66 72  0  0  0  0            999 V2000
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    2.0871    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6696   -0.7096    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7305   -1.6697    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -1.0701    3.4256    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
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  1 22  1  0  0  0  0
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  1 11  1  0  0  0  0
  2  3  1  0  0  0  0
 22  2  1  0  0  0  0
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  3  4  2  0  0  0  0
  4 12  1  0  0  0  0
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  5  6  1  0  0  0  0
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  6  7  2  0  0  0  0
  7 13  1  0  0  0  0
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 61 59  1  0  0  0  0
 62 63  1  6  0  0  0
 64 65  1  0  0  0  0
M  END


  Mrv2104 05262312442D          

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 62 63  1  6  0  0  0
 64 65  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0337295

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H]C(=O)C1=C2\C=C3/N=C(/C=C4\N5[Mg]N2C(\C=C2/N=C([C@@H](CCC(=O)OC\C=C(/C)CCC[C@H](C)CCC[C@H](C)CCCC(C)C)[C@@H]2C)C2=C5C(C(=O)[C@@H]2C(=O)OC)=C4C)=C1C)C(CC)=C3C

> <INCHI_IDENTIFIER>
InChI=1/C54H71N4O6.Mg/c1-12-38-34(7)42-27-46-40(29-59)36(9)41(56-46)26-43-35(8)39(51(57-43)49-50(54(62)63-11)53(61)48-37(10)44(58-52(48)49)28-45(38)55-42)22-23-47(60)64-25-24-33(6)21-15-20-32(5)19-14-18-31(4)17-13-16-30(2)3;/h24,26-32,35,39,50H,12-23,25H2,1-11H3,(H-,55,56,57,58,59,61);/q-1;+2/p-1/b33-24+;/t31-,32-,35+,39+,50-;/s2

> <INCHI_KEY>
QXWRYZIMSXOOPY-KMXYJOOKNA-M

> <FORMULA>
C54H70MgN4O6

> <MOLECULAR_WEIGHT>
895.481

> <EXACT_MASS>
894.51457769

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
135

> <JCHEM_AVERAGE_POLARIZABILITY>
107.46105216071557

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
methyl (5R,8S,9S,10Z,16Z,21Z)-19-ethyl-14-formyl-9,13,18,25-tetramethyl-4-oxo-8-(3-oxo-3-{[(2E,7R,11R)-3,7,11,15-tetramethylhexadec-2-en-1-yl]oxy}propyl)-1,24,26,27-tetraaza-23-magnesaheptacyclo[10.10.2.1^{3,22}.1^{7,10}.1^{17,20}.0^{2,6}.0^{15,24}]heptacosa-2(6),3(25),7(27),10,12,14,16,18,20(26),21-decaene-5-carboxylate

> <JCHEM_LOGP>
11.581600000000002

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
7

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.709826547402058

> <JCHEM_PKA_STRONGEST_BASIC>
4.378742070849544

> <JCHEM_POLAR_SURFACE_AREA>
122.38000000000002

> <JCHEM_REFRACTIVITY>
258.32920000000007

> <JCHEM_ROTATABLE_BOND_COUNT>
22

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
methyl (5R,8S,9S,10Z,16Z,21Z)-19-ethyl-14-formyl-9,13,18,25-tetramethyl-4-oxo-8-(3-oxo-3-{[(2E,7R,11R)-3,7,11,15-tetramethylhexadec-2-en-1-yl]oxy}propyl)-1,24,26,27-tetraaza-23-magnesaheptacyclo[10.10.2.1^{3,22}.1^{7,10}.1^{17,20}.0^{2,6}.0^{15,24}]heptacosa-2(6),3(25),7(27),10,12,14,16,18,20(26),21-decaene-5-carboxylate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 26-MAY-23   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   26-MAY-23         0                                  
HETATM    1  C   UNK     0      -3.078   1.325   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -1.325   3.117   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.000   3.896   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.364   3.117   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       3.117   1.325   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       3.896   0.000   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       3.117  -1.325   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       1.364  -3.117   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -1.325  -3.117   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -3.078  -1.325   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -3.857   0.000   0.000  0.00  0.00           C+0
HETATM   12  N   UNK     0       1.597   1.597   0.000  0.00  0.00           N+0
HETATM   13  N   UNK     0       1.597  -1.597   0.000  0.00  0.00           N+0
HETATM   14  N   UNK     0      -1.558  -1.597   0.000  0.00  0.00           N+0
HETATM   15  C   UNK     0      -3.779   2.727   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      -5.266   3.126   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       2.727   3.818   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       3.857  -2.727   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       5.344  -3.126   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      -2.688   3.818   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       3.857   2.727   0.000  0.00  0.00           C+0
HETATM   22  N   UNK     0      -1.558   1.597   0.000  0.00  0.00           N+0
HETATM   23 Mg   UNK     0       0.000   0.000   0.000  0.00  0.00          Mg+0
HETATM   24  C   UNK     0       5.344   3.126   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       6.433   2.037   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       3.126   5.305   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       0.000  -3.896   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       2.727  -3.818   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       2.329  -5.383   0.000  0.00  0.00           C+0
HETATM   30  O   UNK     0       3.099  -6.717   0.000  0.00  0.00           O+0
HETATM   31  C   UNK     0       0.399  -5.383   0.000  0.00  0.00           C+0
HETATM   32  O   UNK     0      -1.911  -6.717   0.000  0.00  0.00           O+0
HETATM   33  C   UNK     0      -0.371  -6.717   0.000  0.00  0.00           C+0
HETATM   34  O   UNK     0       0.399  -8.051   0.000  0.00  0.00           O+0
HETATM   35  C   UNK     0       1.939  -8.051   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0      -2.688  -3.818   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0      -2.688  -5.358   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0      -4.022  -6.128   0.000  0.00  0.00           C+0
HETATM   39  C   UNK     0      -4.022  -7.668   0.000  0.00  0.00           C+0
HETATM   40  O   UNK     0      -2.688  -8.438   0.000  0.00  0.00           O+0
HETATM   41  O   UNK     0      -5.355  -8.438   0.000  0.00  0.00           O+0
HETATM   42  C   UNK     0      -6.689  -7.668   0.000  0.00  0.00           C+0
HETATM   43  C   UNK     0      -8.023  -8.438   0.000  0.00  0.00           C+0
HETATM   44  C   UNK     0      -9.356  -7.668   0.000  0.00  0.00           C+0
HETATM   45  C   UNK     0     -10.690  -8.438   0.000  0.00  0.00           C+0
HETATM   46  C   UNK     0      -9.356  -6.128   0.000  0.00  0.00           C+0
HETATM   47  C   UNK     0     -12.024  -7.668   0.000  0.00  0.00           C+0
HETATM   48  C   UNK     0     -13.357  -8.438   0.000  0.00  0.00           C+0
HETATM   49  C   UNK     0     -14.691  -7.667   0.000  0.00  0.00           C+0
HETATM   50  C   UNK     0     -16.025  -8.437   0.000  0.00  0.00           C+0
HETATM   51  C   UNK     0     -14.691  -6.127   0.000  0.00  0.00           C+0
HETATM   52  C   UNK     0     -17.358  -7.667   0.000  0.00  0.00           C+0
HETATM   53  C   UNK     0     -18.692  -8.437   0.000  0.00  0.00           C+0
HETATM   54  C   UNK     0     -20.025  -7.667   0.000  0.00  0.00           C+0
HETATM   55  C   UNK     0     -21.359  -8.437   0.000  0.00  0.00           C+0
HETATM   56  C   UNK     0     -20.025  -6.127   0.000  0.00  0.00           C+0
HETATM   57  C   UNK     0     -22.693  -7.667   0.000  0.00  0.00           C+0
HETATM   58  C   UNK     0     -24.027  -8.437   0.000  0.00  0.00           C+0
HETATM   59  C   UNK     0     -25.360  -7.667   0.000  0.00  0.00           C+0
HETATM   60  C   UNK     0     -25.360  -6.127   0.000  0.00  0.00           C+0
HETATM   61  C   UNK     0     -26.694  -8.437   0.000  0.00  0.00           C+0
HETATM   62  C   UNK     0      -3.779  -2.727   0.000  0.00  0.00           C+0
HETATM   63  C   UNK     0      -5.266  -3.126   0.000  0.00  0.00           C+0
HETATM   64  C   UNK     0      -3.087   5.305   0.000  0.00  0.00           C+0
HETATM   65  H   UNK     0      -1.998   6.394   0.000  0.00  0.00           H+0
HETATM   66  O   UNK     0      -4.574   5.704   0.000  0.00  0.00           O+0
CONECT    1   22   15   11                                                  
CONECT    2    3   22   20                                                  
CONECT    3    2    4                                                       
CONECT    4    3   12   17                                                  
CONECT    5    6   12   21                                                  
CONECT    6    5    7                                                       
CONECT    7    6   13   18                                                  
CONECT    8   27   28   13                                                  
CONECT    9   27   14   36                                                  
CONECT   10   11   14   62                                                  
CONECT   11    1   10                                                       
CONECT   12    4    5                                                       
CONECT   13    7    8   23                                                  
CONECT   14    9   10                                                       
CONECT   15    1   20   16                                                  
CONECT   16   15                                                            
CONECT   17    4   21   26                                                  
CONECT   18    7   28   19                                                  
CONECT   19   18                                                            
CONECT   20    2   15   64                                                  
CONECT   21    5   17   24                                                  
CONECT   22    1    2   23                                                  
CONECT   23   13   22                                                       
CONECT   24   21   25                                                       
CONECT   25   24                                                            
CONECT   26   17                                                            
CONECT   27    8    9   31                                                  
CONECT   28    8   18   29                                                  
CONECT   29   28   31   30                                                  
CONECT   30   29                                                            
CONECT   31   27   29   33                                                  
CONECT   32   33                                                            
CONECT   33   31   32   34                                                  
CONECT   34   33   35                                                       
CONECT   35   34                                                            
CONECT   36    9   62   37                                                  
CONECT   37   38   36                                                       
CONECT   38   37   39                                                       
CONECT   39   38   41   40                                                  
CONECT   40   39                                                            
CONECT   41   39   42                                                       
CONECT   42   41   43                                                       
CONECT   43   42   44                                                       
CONECT   44   43   45   46                                                  
CONECT   45   44   47                                                       
CONECT   46   44                                                            
CONECT   47   45   48                                                       
CONECT   48   47   49                                                       
CONECT   49   48   50   51                                                  
CONECT   50   49   52                                                       
CONECT   51   49                                                            
CONECT   52   50   53                                                       
CONECT   53   52   54                                                       
CONECT   54   53   55   56                                                  
CONECT   55   54   57                                                       
CONECT   56   54                                                            
CONECT   57   55   58                                                       
CONECT   58   57   59                                                       
CONECT   59   58   60   61                                                  
CONECT   60   59                                                            
CONECT   61   59                                                            
CONECT   62   10   36   63                                                  
CONECT   63   62                                                            
CONECT   64   20   66   65                                                  
CONECT   65   64                                                            
CONECT   66   64                                                            
MASTER        0    0    0    0    0    0    0    0   66    0  144    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₅₄H₇₀MgN₄O₆

Average Mass

895.4810 Da

Monoisotopic Mass

894.51458 Da

IUPAC Name

methyl (5R,8S,9S,10Z,16Z,21Z)-19-ethyl-14-formyl-9,13,18,25-tetramethyl-4-oxo-8-(3-oxo-3-{[(2E,7R,11R)-3,7,11,15-tetramethylhexadec-2-en-1-yl]oxy}propyl)-1,24,26,27-tetraaza-23-magnesaheptacyclo[10.10.2.1^{3,22}.1^{7,10}.1^{17,20}.0^{2,6}.0^{15,24}]heptacosa-2(6),3(25),7(27),10,12,14,16,18,20(26),21-decaene-5-carboxylate

Traditional Name

CAS Registry Number

Not Available

SMILES

[H]C(=O)C1=C2\C=C3/N=C(/C=C4\N5[Mg]N2C(\C=C2/N=C([C@@H](CCC(=O)OC\C=C(/C)CCC[C@H](C)CCC[C@H](C)CCCC(C)C)[C@@H]2C)C2=C5C(C(=O)[C@@H]2C(=O)OC)=C4C)=C1C)C(CC)=C3C

InChI Identifier

InChI=1/C54H71N4O6.Mg/c1-12-38-34(7)42-27-46-40(29-59)36(9)41(56-46)26-43-35(8)39(51(57-43)49-50(54(62)63-11)53(61)48-37(10)44(58-52(48)49)28-45(38)55-42)22-23-47(60)64-25-24-33(6)21-15-20-32(5)19-14-18-31(4)17-13-16-30(2)3;/h24,26-32,35,39,50H,12-23,25H2,1-11H3,(H-,55,56,57,58,59,61);/q-1;+2/p-1/b33-24+;/t31-,32-,35+,39+,50-;/s2

InChI Key

QXWRYZIMSXOOPY-KMXYJOOKNA-M

Experimental Spectra

Not Available

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Not Available

Chemical Taxonomy

Description

This compound belongs to the class of organic compounds known as chlorins. These are large heterocyclic aromatic ring systems consisting, at the core, of three pyrroles and one pyrroline coupled through four methine linkages.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Tetrapyrroles and derivatives

Sub Class

Chlorins

Direct Parent

Chlorins

Alternative Parents

Substituents

Chlorin
Metallotetrapyrrole skeleton
Phorbine skeleton
Diterpenoid
Aryl ketone
Aryl alkyl ketone
Fatty acid ester
Aryl-aldehyde
Fatty acyl
1,3-dicarbonyl compound
Substituted pyrrole
Dicarboxylic acid or derivatives
Heteroaromatic compound
Methyl ester
Pyrrole
Carboxylic acid ester
Ketone
Azacycle
Carboxylic acid derivative
Organic salt
Organic oxide
Organonitrogen compound
Aldehyde
Organic oxygen compound
Organooxygen compound
Organic nitrogen compound
Organic zwitterion
Carbonyl group
Hydrocarbon derivative
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

methyl ester (CHEBI:38199 )
chlorophyll (CHEBI:38199 )

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	11.58	ChemAxon
pKa (Strongest Acidic)	11.71	ChemAxon
pKa (Strongest Basic)	4.38	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	122.38 Å²	ChemAxon
Rotatable Bond Count	22	ChemAxon
Refractivity	258.33 m³·mol⁻¹	ChemAxon
Polarizability	107.46 Å³	ChemAxon
Number of Rings	7	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

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

Chlorophyll d

METLIN ID

Not Available

PubChem Compound

Not Available

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Gisriel CJ, Ranepura G, Brudvig GW, Gunner MR: Assignment of chlorophyll d in the Chl(D1) site of the electron transfer chain of far-red light acclimated photosystem II supported by MCCE binding calculations. Biochim Biophys Acta Bioenerg. 2024 Nov 1;1865(4):149496. doi: 10.1016/j.bbabio.2024.149496. Epub 2024 Jul 20. [PubMed:39038640 ]
Ulrich NJ, Shen G, Bryant DA, Miller SR: Ecological diversification of a cyanobacterium through divergence of its novel chlorophyll d-based light-harvesting system. Curr Biol. 2024 Jul 8;34(13):2972-2979.e4. doi: 10.1016/j.cub.2024.05.022. Epub 2024 Jun 7. [PubMed:38851184 ]
Shen L, Gao Y, Tang K, Qi R, Fu L, Chen JH, Wang W, Ma X, Li P, Chen M, Kuang T, Zhang X, Shen JR, Wang P, Han G: Structure of a unique PSII-Pcb tetrameric megacomplex in a chlorophyll d-containing cyanobacterium. Sci Adv. 2024 Feb 23;10(8):eadk7140. doi: 10.1126/sciadv.adk7140. Epub 2024 Feb 23. [PubMed:38394197 ]
Elias E, Brache K, Schafers J, Croce R: Coloring Outside the Lines: Exploiting Pigment-Protein Synergy for Far-Red Absorption in Plant Light-Harvesting Complexes. J Am Chem Soc. 2024 Feb 7;146(5):3508-3520. doi: 10.1021/jacs.3c13373. Epub 2024 Jan 29. [PubMed:38286009 ]
Ko JT, Li YY, Chen PY, Liu PY, Ho MY: Use of 16S rRNA gene sequences to identify cyanobacteria that can grow in far-red light. Mol Ecol Resour. 2024 Jan;24(1):e13871. doi: 10.1111/1755-0998.13871. Epub 2023 Sep 29. [PubMed:37772760 ]

Showing NP-Card for Chlorophyll d (NP0337295)

MOL for NP0337295 (Chlorophyll d)

3D MOL for NP0337295 (Chlorophyll d)

3D SDF for NP0337295 (Chlorophyll d)

3D-SDF for NP0337295 (Chlorophyll d)

PDB for NP0337295 (Chlorophyll d)

3D PDB for NP0337295 (Chlorophyll d)

SMILES for NP0337295 (Chlorophyll d)

INCHI for NP0337295 (Chlorophyll d)

Structure for NP0337295 (Chlorophyll d)

3D Structure for NP0337295 (Chlorophyll d)