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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-09-11 22:29:43 UTC
Update Date2022-03-07 02:55:15 UTC
HMDB IDHMDB0037256
Secondary Accession Numbers
  • HMDB37256
Metabolite Identification
Common NameChlorophyll d
DescriptionChlorophyll d is widely distributed photosynthetic pigment. Chlorophyll is a chlorin pigment, which is structurally similar to and produced through the same metabolic pathway as other porphyrin pigments such as heme. At the center of the chlorin ring is a magnesium ion. For the structures depicted in this article, some of the ligands attached to the Mg2+ center are omitted for clarity. The chlorin ring can have several different side chains, usually including a long phytol chain. There are a few different forms that occur naturally, but the most widely distributed form in terrestrial plants is chlorophyll a. The general structure of chlorophyll a was elucidated by Hans Fischer in 1940, and by 1960, when most of the stereochemistry of chlorophyll a was known, Robert Burns Woodward published a total synthesis of the molecule as then known. In 1967, the last remaining stereochemical elucidation was completed by Ian Fleming, and in 1990 Woodward and co-authors published an updated synthesis. Chlorophyll is a green pigment found in most plants, algae, and cyanobacteria. Its name is derived from the Greek (chloros "green") and (phyllon "leaf"). Chlorophyll absorbs light most strongly in the blue and red but poorly in the green portions of the electromagnetic spectrum, hence the green colour of chlorophyll-containing tissues such as plant leaves. Chlorophyll itself is bound to proteins and can transfer the absorbed energy in the required direction. Protochlorophyllide, differently, mostly occur in the free form and under light conditions act as photosensitizer, forming highly toxic free radicals. Hence plants need an efficient mechanism of regulating the amount of chlorophyll precursor. In angiosperms, this is done at the step of aminolevulinic acid (ALA), one of the intermediate compounds in the biosynthesis pathway. Plants that are fed by ALA accumulate high and toxic levels of protochlorophyllide, so do the mutants with the damaged regulatory system. Chlorosis is a condition in which leaves produce insufficient chlorophyll, turning them yellow. Chlorosis can be caused by a nutrient deficiency including iron - called iron chlorosis, or in a shortage of magnesium or nitrogen. Soil pH sometimes play a role in nutrient-caused chlorosis, many plants are adapted to grow in soils with specific pHs and their ability to absorb nutrients from the soil can be dependent on the soil pH. Chlorosis can also be caused by pathogens including viruses, bacteria and fungal infections or sap sucking insects.
Structure
Data?1563863001
Synonyms
ValueSource
CHL D CPDMeSH, HMDB
Chemical FormulaC54H70MgN4O6
Average Molecular Weight895.462
Monoisotopic Molecular Weight894.51457789
IUPAC Namemethyl (5R,8S,9S,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 Namemethyl (5R,8S,9S,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
CAS Registry Number519-63-1
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=1S/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-;/m1./s1
InChI KeyQXWRYZIMSXOOPY-SKHCYZARSA-M
Chemical Taxonomy
Description 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.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassTetrapyrroles and derivatives
Sub ClassChlorins
Direct ParentChlorins
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 FrameworkAromatic heteropolycyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
ProcessNot Available
Role
Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility0.0016 g/LALOGPS
logP7.94ALOGPS
logP11.58ChemAxon
logS-6.2ALOGPS
pKa (Strongest Acidic)3.94ChemAxon
pKa (Strongest Basic)7.05ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count6ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area122.38 ŲChemAxon
Rotatable Bond Count22ChemAxon
Refractivity258.33 m³·mol⁻¹ChemAxon
Polarizability107.46 ųChemAxon
Number of Rings7ChemAxon
BioavailabilityNoChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleYesChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
AllCCS[M+H]+316.732859911
AllCCS[M+H-H2O]+316.432859911
AllCCS[M+NH4]+316.832859911
AllCCS[M+Na]+316.932859911
AllCCS[M-H]-247.932859911
AllCCS[M+Na-2H]-253.532859911
AllCCS[M+HCOO]-259.632859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
Chlorophyll d[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)=C3C8021.2Standard polar33892256
Chlorophyll d[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)=C3C5806.5Standard non polar33892256
Chlorophyll d[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)=C3C6212.8Semi standard non polar33892256
Spectra

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Chlorophyll d 10V, Positive-QTOFsplash10-002b-0050030090-69900e048823123741e72019-02-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Chlorophyll d 20V, Positive-QTOFsplash10-004i-4490040010-7103ef102388fba93e4c2019-02-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Chlorophyll d 40V, Positive-QTOFsplash10-004j-3290412210-5ba49ac0055674044b352019-02-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Chlorophyll d 10V, Negative-QTOFsplash10-0007-0020051090-0b23878f85f589cc8ed32019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Chlorophyll d 20V, Negative-QTOFsplash10-014j-0020092030-c2ce2da8a3c58e91e4f92019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Chlorophyll d 40V, Negative-QTOFsplash10-0a4r-1050090010-85e83c782b016fa71bf12019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Chlorophyll d 10V, Negative-QTOFsplash10-0006-0000000090-042304a0846c1954ae922021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Chlorophyll d 20V, Negative-QTOFsplash10-00kf-0000090030-68a7438ff7b08560c7ed2021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Chlorophyll d 40V, Negative-QTOFsplash10-0btc-0000090010-562893810c73dfafb91d2021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Chlorophyll d 10V, Positive-QTOFsplash10-0002-3000013190-68601bfb7d3cd9986f832021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Chlorophyll d 20V, Positive-QTOFsplash10-014i-9400012400-62ff39de362b0f31d55a2021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Chlorophyll d 40V, Positive-QTOFsplash10-007k-9400021000-1ab9d9e5129743e3c9412021-09-24Wishart LabView Spectrum
Biological Properties
Cellular Locations
  • Membrane
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB016268
KNApSAcK IDNot Available
Chemspider ID16736116
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkChlorophyll d
METLIN IDNot Available
PubChem Compound16070025
PDB IDNot Available
ChEBI ID38199
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1440221
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. (). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .