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Showing NP-Card for Gramine (NP0332248)

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Record Information
Version2.0
Created at2023-12-21 00:01:52 UTC
Updated at2024-09-03 04:18:35 UTC
NP-MRD IDNP0332248
Natural Product DOIhttps://doi.org/10.57994/1439
Secondary Accession NumbersNone
Natural Product Identification
Common NameGramine
Description3-(Dimethylaminomethyl)indole, also known as donaxin or (1H-indol-3-ylmethyl)dimethylamine, belongs to the class of organic compounds known as 3-alkylindoles. 3-Alkylindoles are compounds containing an indole moiety that carries an alkyl chain at the 3-position. An aminoalkylindole that is indole carrying a dimethylaminomethyl substituent at postion 3. 3-(Dimethylaminomethyl)indole is a very strong basic compound (based on its pKa). Outside of the human body, 3-(Dimethylaminomethyl)indole has been detected, but not quantified in, several different foods, such as barley, brassicas, cereals and cereal products, common wheats, and lupines. Gramine was first documented in 2013 (PMID: 23700450). This could make 3-(dimethylaminomethyl)indole a potential biomarker for the consumption of these foods (PMID: 24332729) (PMID: 24979400) (PMID: 25149234) (PMID: 25281166) (PMID: 26920698) (PMID: 27037659).
Structure
Thumb
MOLSDFPDBSMILESInChI

MOL for NP0332248 (Gramine)


  Mrv1652305261923562D          

 13 14  0  0  0  0            999 V2000
   -0.1781   -0.8853    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4752    0.5124    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523    1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523    1.9354    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    0.6979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    2.3479    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6538    1.5229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8838    0.0709    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387    0.8555    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233    1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233    1.9354    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387    2.1904    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0768   -0.1006    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  4  3  2  0  0  0  0
  5  3  1  0  0  0  0
  6  4  1  0  0  0  0
  9  7  2  0  0  0  0
  9  8  1  0  0  0  0
 10  5  2  0  0  0  0
 10  9  1  0  0  0  0
 11  6  2  0  0  0  0
 11 10  1  0  0  0  0
 12  7  1  0  0  0  0
 12 11  1  0  0  0  0
 13  1  1  0  0  0  0
 13  2  1  0  0  0  0
 13  8  1  0  0  0  0
M  END
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3D MOL for NP0332248 (Gramine)

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3D SDF for NP0332248 (Gramine)

  Mrv1652305261923562D          

 13 14  0  0  0  0            999 V2000
   -0.1781   -0.8853    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4752    0.5124    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523    1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523    1.9354    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    0.6979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    2.3479    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6538    1.5229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8838    0.0709    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387    0.8555    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233    1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233    1.9354    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387    2.1904    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0768   -0.1006    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  4  3  2  0  0  0  0
  5  3  1  0  0  0  0
  6  4  1  0  0  0  0
  9  7  2  0  0  0  0
  9  8  1  0  0  0  0
 10  5  2  0  0  0  0
 10  9  1  0  0  0  0
 11  6  2  0  0  0  0
 11 10  1  0  0  0  0
 12  7  1  0  0  0  0
 12 11  1  0  0  0  0
 13  1  1  0  0  0  0
 13  2  1  0  0  0  0
 13  8  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0332248

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CN(C)CC1=CNC2=CC=CC=C12

> <INCHI_IDENTIFIER>
InChI=1S/C11H14N2/c1-13(2)8-9-7-12-11-6-4-3-5-10(9)11/h3-7,12H,8H2,1-2H3

> <INCHI_KEY>
OCDGBSUVYYVKQZ-UHFFFAOYSA-N

> <FORMULA>
C11H14N2

> <MOLECULAR_WEIGHT>
174.2423

> <EXACT_MASS>
174.115698458

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
27

> <JCHEM_AVERAGE_POLARIZABILITY>
20.240085262918186

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
[(1H-indol-3-yl)methyl]dimethylamine

> <ALOGPS_LOGP>
2.01

> <JCHEM_LOGP>
2.0134045759999997

> <ALOGPS_LOGS>
-1.71

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_ACIDIC>
15.973408350193871

> <JCHEM_PKA_STRONGEST_BASIC>
8.985716789273653

> <JCHEM_POLAR_SURFACE_AREA>
19.03

> <JCHEM_REFRACTIVITY>
55.687200000000004

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.43e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
gramin

> <JCHEM_VEBER_RULE>
1

$$$$

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3D-SDF for NP0332248 (Gramine)
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PDB for NP0332248 (Gramine)
HEADER    PROTEIN                                 26-MAY-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   26-MAY-19         0                                  
HETATM    1  C   UNK     0      -0.332  -1.653   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -0.887   0.956   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       6.258   2.073   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       6.258   3.613   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       4.924   1.303   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       4.924   4.383   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       1.220   2.843   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       1.650   0.132   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       2.126   1.597   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       3.590   2.073   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       3.590   3.613   0.000  0.00  0.00           C+0
HETATM   12  N   UNK     0       2.126   4.089   0.000  0.00  0.00           N+0
HETATM   13  N   UNK     0       0.143  -0.188   0.000  0.00  0.00           N+0
CONECT    1   13                                                            
CONECT    2   13                                                            
CONECT    3    4    5                                                       
CONECT    4    3    6                                                       
CONECT    5    3   10                                                       
CONECT    6    4   11                                                       
CONECT    7    9   12                                                       
CONECT    8    9   13                                                       
CONECT    9    7    8   10                                                  
CONECT   10    5    9   11                                                  
CONECT   11    6   10   12                                                  
CONECT   12    7   11                                                       
CONECT   13    1    2    8                                                  
MASTER        0    0    0    0    0    0    0    0   13    0   28    0
END

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3D PDB for NP0332248 (Gramine)
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SMILES for NP0332248 (Gramine)
CN(C)CC1=CNC2=CC=CC=C12
Download
INCHI for NP0332248 (Gramine)
InChI=1S/C11H14N2/c1-13(2)8-9-7-12-11-6-4-3-5-10(9)11/h3-7,12H,8H2,1-2H3
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View in JSmol
Synonyms
ValueSource
(1H-indol-3-Ylmethyl)dimethylamineChEBI
3-(N,N-Dimethylaminomethyl)indoleChEBI
3-[(Dimethylamino)methyl]indoleChEBI
beta-DimethylaminomethylindoleChEBI
DonaxinChEBI
DonaxineChEBI
GraminChEBI
indol-3-YlmethyldimethylamineChEBI
N,N-Dimethyl-1H-indole-3-methanamineChEBI
(1H-indol-3-yl)-N,N-DimethylmethanamineKegg
b-DimethylaminomethylindoleGenerator
Β-dimethylaminomethylindoleGenerator
(1H-indol-3-Ylmethyl)-dimethyl-amineHMDB
(indol-3-Ylmethyl)dimethylamineHMDB
1-(1H-indol-3-yl)-N,N-DimethylmethanamineHMDB
1H-indol-3-yl-N,N-DimethylmethanamineHMDB
3-((Dimethylamino)methyl)-indoleHMDB
3-Dimethylaminomethylindol (gramin)HMDB
3-[(Dimethylamino)methyl]-indoleHMDB
b-(Dimethylaminomethyl)indoleHMDB
beta -DimethylaminomethylindoleHMDB
DoranineHMDB
Indolalkylamine der.HMDB
N,N-Dimethyl-1H-indole-3-methanamine, 9ciHMDB
N,N-Dimethyl-1H-indole-3-methylamineHMDB
3-(Dimethylaminomethyl)indoleChEBI
Chemical FormulaC11H14N2
Average Mass174.2423 Da
Monoisotopic Mass174.11570 Da
IUPAC Name[(1H-indol-3-yl)methyl]dimethylamine
Traditional Namegramin
CAS Registry NumberNot Available
SMILES
CN(C)CC1=CNC2=CC=CC=C12
InChI Identifier
InChI=1S/C11H14N2/c1-13(2)8-9-7-12-11-6-4-3-5-10(9)11/h3-7,12H,8H2,1-2H3
InChI KeyOCDGBSUVYYVKQZ-UHFFFAOYSA-N
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
HSQC NMR[1H, 13C] NMR Spectrum (2D, 600 MHz, CD3OD, experimental)bgnzk@missouri.eduMU Metabolomics Center, University of Missouri, Columbia. MO, USADr. Bharat Goel2024-05-02View Spectrum
HMBC NMR[1H, 13C] NMR Spectrum (2D, 600 MHz, CD3OD, experimental)bgnzk@missouri.eduMU Metabolomics Center, University of Missouri, Columbia. MO, USADr. Bharat Goel2024-05-02View Spectrum
COSY NMR[1H, 1H] NMR Spectrum (2D, 600 MHz, CD3OD, experimental)bgnzk@missouri.eduMU Metabolomics Center, University of Missouri, Columbia. MO, USADr. Bharat Goel2024-05-02View Spectrum
1D NMR13C NMR Spectrum (1D, 201 MHz, CD3OD, experimental)bgnzk@missouri.eduMU Metabolomics Center, University of Missouri, Columbia. MO, USADr. Bharat Goel2024-05-02View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, CD3OD, experimental)bgnzk@missouri.eduMU Metabolomics Center, University of Missouri, Columbia. MO, USADr. Bharat Goel2024-05-02View Spectrum
1D NMR13C NMR Spectrum (1D, 25.16 MHz, CDCl3, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Predicted Spectra
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
Chemical Shift Submissions
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR1H NMR Spectrum (1D, 600.133705802, CD3OD, simulated)bgnzk@missouri.eduSumner Lab, MU Metabolomics Center, University of Missouri, Columbia. MO, USADr. Bharat Goel2024-05-02View Spectrum
Species
Species of OriginNot Available
Chemical Taxonomy
Description Belongs to the class of organic compounds known as 3-alkylindoles. 3-Alkylindoles are compounds containing an indole moiety that carries an alkyl chain at the 3-position.
KingdomOrganic compounds  
Super ClassOrganoheterocyclic compounds  
ClassIndoles and derivatives  
Sub ClassIndoles  
Direct Parent3-alkylindoles  
Alternative Parents
Substituents
  • 3-alkylindole
    • 

  • Aralkylamine
    • 

  • Benzenoid
    • 

  • Substituted pyrrole
    • 

  • Heteroaromatic compound
    • 

  • Pyrrole
    • 

  • Tertiary aliphatic amine
    • 

  • Tertiary amine
    • 

  • Azacycle
    • 

  • Organic nitrogen compound
    • 

  • Organopnictogen compound
    • 

  • Hydrocarbon derivative
    • 

  • Organonitrogen compound
    • 

  • Amine
    • 

  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External Descriptors
Physical Properties
StateNot Available
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP2.01ALOGPS
logP2.01ChemAxon
logS-1.7ALOGPS
pKa (Strongest Acidic)15.97ChemAxon
pKa (Strongest Basic)8.99ChemAxon
Physiological Charge1ChemAxon
Hydrogen Acceptor Count1ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area19.03 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity55.69 m³·mol⁻¹ChemAxon
Polarizability20.24 ųChemAxon
Number of Rings2ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0035762  
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB014498  
KNApSAcK IDC00001411  
Chemspider ID6625  
KEGG Compound IDC08304  
BioCyc IDCPD-8915  
BiGG IDNot Available
Wikipedia LinkGramine  
METLIN IDNot Available
PubChem Compound6890  
PDB IDNot Available
ChEBI ID28948  
Good Scents IDNot Available
References
General References
  1. Sun XQ, Zhang MX, Yu JY, Jin Y, Ling B, Du JP, Li GH, Qin QM, Cai QN: Glutathione S-transferase of brown planthoppers (Nilaparvata lugens) is essential for their adaptation to gramine-containing host plants. PLoS One. 2013 May 20;8(5):e64026. doi: 10.1371/journal.pone.0064026. Print 2013. [PubMed:23700450  ] 
  2. Laue P, Bahrs H, Chakrabarti S, Steinberg CE: Natural xenobiotics to prevent cyanobacterial and algal growth in freshwater: contrasting efficacy of tannic acid, gallic acid, and gramine. Chemosphere. 2014 Jun;104:212-20. doi: 10.1016/j.chemosphere.2013.11.029. Epub 2013 Dec 13. [PubMed:24332729  ] 
  3. Wei Y, Shi L, Wang K, Liu M, Yang Q, Yang Z, Ke S: Discovery of gramine derivatives that inhibit the early stage of EV71 replication in vitro. Molecules. 2014 Jun 27;19(7):8949-64. doi: 10.3390/molecules19078949. [PubMed:24979400  ] 
  4. Zhang M, Fang T, Pu G, Sun X, Zhou X, Cai Q: Xenobiotic metabolism of plant secondary compounds in the English grain aphid, Sitobion avenae (F.) (Hemiptera: Aphididae). Pestic Biochem Physiol. 2013 Sep;107(1):44-9. doi: 10.1016/j.pestbp.2013.05.002.  Epub 2013 May 17. [PubMed:25149234  ] 
  5. Wu Q, Shi H, Ma Y, Adams C, Eichholz T, Timmons T, Jiang H: Determination of secondary and tertiary amines as N-nitrosamine precursors in drinking water system using ultra-fast liquid chromatography-tandem mass spectrometry. Talanta. 2015 Jan;131:736-41. doi: 10.1016/j.talanta.2014.08.003. Epub 2014 Aug 11. [PubMed:25281166  ] 
  6. Liu SL, Wang WW, Liu F, Li HY, Liu JS, Yang WD: Removal of Two Species of Harmful Algae Using Gramine Modified Montmorillonite. Bull Environ Contam Toxicol. 2016 Apr;96(4):540-3. doi:  10.1007/s00128-016-1758-y. Epub 2016 Feb 27. [PubMed:26920698  ] 
  7. West DM, Wu Q, Donovan A, Shi H, Ma Y, Jiang H, Wang J: N-nitrosamine formation by monochloramine, free chlorine, and peracetic acid disinfection with presence of amine precursors in drinking water system. Chemosphere. 2016 Jun;153:521-7. doi: 10.1016/j.chemosphere.2016.03.035. Epub  2016 Mar 31. [PubMed:27037659  ] 
  8. Popp D, Harms H, Strauber H: The alkaloid gramine in the anaerobic digestion process-inhibition and adaptation of the methanogenic community. Appl Microbiol Biotechnol. 2016 Aug;100(16):7311-22. doi:  10.1007/s00253-016-7571-z. Epub 2016 Apr 30. [PubMed:27138201  ] 
  9. Lulinski P, Klejn D, Maciejewska D: Synthesis and characterization of imprinted sorbent for separation of gramine from bovine serum albumin. Mater Sci Eng C Mater Biol Appl. 2016 Aug 1;65:400-7. doi:  10.1016/j.msec.2016.04.051. Epub 2016 Apr 19. [PubMed:27157767  ] 
  10. Liu F, He ZB, Li HY, Liu JS, Yang WD: Inhibition of five natural products from Chinese herbs on the growth of Chattonella marina. Environ Sci Pollut Res Int. 2016 Sep;23(17):17793-800. doi:  10.1007/s11356-016-6755-5. Epub 2016 Jun 1. [PubMed:27250087  ]