Hmdb loader
Survey
You are using an unsupported browser. Please upgrade your browser to a newer version to get the best experience on Human Metabolome Database.
Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-09-11 17:41:17 UTC
Update Date2022-03-07 02:52:50 UTC
HMDB IDHMDB0031148
Secondary Accession Numbers
  • HMDB31148
Metabolite Identification
Common NameProtochlorophyllide
DescriptionProtochlorophyllide is found in fruits. Protochlorophyllide is isolated from the seed husks of Cucurbita pepo Chlorophyll itself is bound to proteins and can transfer the absorbed energy in the required direction. Protochlorophyllide, differently, mostly occurs in the free form and under light conditions acts 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 D-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. Despite of numerous past attempts to find the mutant that overacumulates protochlorophyllide under usual conditions, only one such gene (flu) is currently (2009) known. Flu (first described in ) is a nuclear - encoded, chloroplast - located protein that appears containing only protein - protein interaction sites. It is currently not know which other proteins interact through this linker. The regulatory protein is a transmembrane protein that is located in the thylakoid membrane. Later it was discovered that Tigrina mutants in barley, known long time ago, are also mutated in the same gene It is not obvious why no mutants of any other gene were observed; maybe mutations in other proteins, involved into the regulatory chain, are fatal. Flu is a single gene, not a member of the gene family. Protochlorophyllide , more accurate monovinyl protochlorophyllide, is an immediate precursor of chlorophyll a that lacks the phytol side chain of chlorophyll. Unlike chlorophyll, protochlorophyllide is highly fluorescent; mutants that accumulate it glow in red if irradiated by the blue lightIn Angiosperms, the last step, conversion of protochlorophyllide to chlorophyll, is light - dependent and such plants are pale (etiolated) if grown in the darkness. Gymnosperms, algae, and photosynthetic bacteria additionally have another, light - independent enzyme and grow green in the darkness as well. The enzyme that converts protochlorophyllide to chlorophyll is protochlorophyllide reductase , EC 1.3.1.33. There are two structurally unrelated proteins with this activity: the light - dependent and the dark - operative. The light dependent reductase needs light to operate. The dark - operative version is a completely different protein, consisting of three subunits that exhibit significant sequence similarity to the three subunits of nitrogenase, which catalyzes the formation of ammonia from dinitrogen. This enzyme might be evolutionary older but (being similar to nitrogenase) is highly sensitive to free oxygen and does not work if its concentration exceeds about 3 %. Hence the alternative, light dependent version needed to evolve
Structure
Data?1563862088
Synonyms
ValueSource
Protochlorophyllide aChEBI
{3-[(21R)-14-ethyl-21-(methoxycarbonyl)-4,8,13,18-tetramethyl-20-oxo-9-vinyl-3,4-didehydrophorbin-3-yl-kappa(4)N(23),N(24),N(25),N(26)]propanoato(2-)}magnesiumChEBI
Chemical FormulaC35H32MgN4O5
Average Molecular Weight612.969
Monoisotopic Molecular Weight612.22231185
IUPAC Name(5R)-23-(2-carboxyethyl)-17-ethenyl-12-ethyl-5-(methoxycarbonyl)-8,13,18,22-tetramethyl-6-oxo-2,25lambda5,26lambda5,27-tetraaza-1-magnesanonacyclo[12.11.1.1^{1,16}.0^{2,9}.0^{3,7}.0^{4,24}.0^{11,26}.0^{21,25}.0^{19,27}]heptacosa-3(7),4(24),8,10,12,14(26),15,17,19,21(25),22-undecaene-25,26-bis(ylium)-1,1-diuide
Traditional Name(5R)-23-(2-carboxyethyl)-17-ethenyl-12-ethyl-5-(methoxycarbonyl)-8,13,18,22-tetramethyl-6-oxo-2,25lambda5,26lambda5,27-tetraaza-1-magnesanonacyclo[12.11.1.1^{1,16}.0^{2,9}.0^{3,7}.0^{4,24}.0^{11,26}.0^{21,25}.0^{19,27}]heptacosa-3(7),4(24),8,10,12,14(26),15,17,19,21(25),22-undecaene-25,26-bis(ylium)-1,1-diuide
CAS Registry Number14751-08-7
SMILES
CCC1=C(C)C2=[N+]3C1=CC1=C(C)C4=C5N1[Mg--]31N3C(=CC6=[N+]1C(C(CCC(O)=O)=C6C)=C5[C@@H](C(=O)OC)C4=O)C(C)=C(C=C)C3=C2
InChI Identifier
InChI=1S/C35H34N4O5.Mg/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;/h8,12-14,31H,1,9-11H2,2-7H3,(H3,36,37,38,39,40,41,42);/q;+2/p-2/b22-12-,23-13-,24-12-,25-14-,26-13-,27-14-,32-30-;/t31-;/m1./s1
InChI KeyQBPCOMNNISRCTC-KKNVGXODSA-L
Chemical Taxonomy
Description Belongs to the class of organic compounds known as metalloporphyrins. These are polycyclic compounds containing a porphyrin moiety and a metal atom.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassTetrapyrroles and derivatives
Sub ClassMetallotetrapyrroles
Direct ParentMetalloporphyrins
Alternative ParentsNot Available
SubstituentsNot Available
Molecular FrameworkNot Available
External DescriptorsNot Available
Ontology
Not AvailableNot Available
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 Solubility0.042 g/LALOGPS
logP-0.47ALOGPS
logP-0.091ChemAxon
logS-5.6ALOGPS
pKa (Strongest Acidic)3.68ChemAxon
pKa (Strongest Basic)-7.1ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area98.29 ŲChemAxon
Rotatable Bond Count7ChemAxon
Refractivity173.94 m³·mol⁻¹ChemAxon
Polarizability69.78 ųChemAxon
Number of Rings9ChemAxon
BioavailabilityYesChemAxon
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]+235.432859911
AllCCS[M+H-H2O]+234.332859911
AllCCS[M+NH4]+236.332859911
AllCCS[M+Na]+236.632859911
AllCCS[M-H]-230.532859911
AllCCS[M+Na-2H]-232.332859911
AllCCS[M+HCOO]-234.432859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
ProtochlorophyllideCCC1=C(C)C2=[N+]3C1=CC1=C(C)C4=C5N1[Mg--]31N3C(=CC6=[N+]1C(C(CCC(O)=O)=C6C)=C5[C@@H](C(=O)OC)C4=O)C(C)=C(C=C)C3=C27465.9Standard polar33892256
ProtochlorophyllideCCC1=C(C)C2=[N+]3C1=CC1=C(C)C4=C5N1[Mg--]31N3C(=CC6=[N+]1C(C(CCC(O)=O)=C6C)=C5[C@@H](C(=O)OC)C4=O)C(C)=C(C=C)C3=C24359.5Standard non polar33892256
ProtochlorophyllideCCC1=C(C)C2=[N+]3C1=CC1=C(C)C4=C5N1[Mg--]31N3C(=CC6=[N+]1C(C(CCC(O)=O)=C6C)=C5[C@@H](C(=O)OC)C4=O)C(C)=C(C=C)C3=C25010.6Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
Protochlorophyllide,1TMS,isomer #1C=CC1=C(C)C2=CC3=[N+]4C(=C5C6=C(C(=O)[C@@H]5C(=O)OC)C(C)=C5C=C7C(CC)=C(C)C8=[N+]7[Mg-2]4(N56)N2C1=C8)C(CCC(=O)O[Si](C)(C)C)=C3C4885.7Semi standard non polar33892256
Protochlorophyllide,1TBDMS,isomer #1C=CC1=C(C)C2=CC3=[N+]4C(=C5C6=C(C(=O)[C@@H]5C(=O)OC)C(C)=C5C=C7C(CC)=C(C)C8=[N+]7[Mg-2]4(N56)N2C1=C8)C(CCC(=O)O[Si](C)(C)C(C)(C)C)=C3C5079.4Semi standard non polar33892256
Spectra

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-30Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-30Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-30Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-30Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-30Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-30Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-30Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-30Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-30Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-30Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-30Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-30Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-30Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-30Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-30Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-30Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-30Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-30Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-30Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-30Wishart LabView Spectrum
Biological Properties
Cellular Locations
  • Cytoplasm
  • Extracellular
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 IDNot Available
KNApSAcK IDC00057075
Chemspider ID388880
KEGG Compound IDC02880
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkProtochlorophyllide
METLIN IDNot Available
PubChem CompoundNot Available
PDB IDNot Available
ChEBI ID16673
Food Biomarker OntologyNot Available
VMH IDPROTOCHLOROPH
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Meskauskiene R, Nater M, Goslings D, Kessler F, op den Camp R, Apel K: FLU: a negative regulator of chlorophyll biosynthesis in Arabidopsis thaliana. Proc Natl Acad Sci U S A. 2001 Oct 23;98(22):12826-31. Epub 2001 Oct 16. [PubMed:11606728 ]
  2. (). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .