NP-MRD: Showing NP-Card for Germine (NP0051297)

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Record Information

Version

2.0

Created at

2022-04-27 22:40:40 UTC

Updated at

2022-04-27 22:40:40 UTC

NP-MRD ID

NP0051297

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Germine

Description

Germine, also known as germabenzene, belongs to the class of organic compounds known as cerveratrum-type alkaloids. These are steroidal alkaloids containing the cevane (23-methyl-4- azahexacyclo[12.11.0.0^{2,11}.0^{4,9}.0^{15,24}.0^{18,23}]Pentacosane) moiety, which is a six ring system. Cerveratrum alkaloids have 7-9 oxygen atoms and occur as free alkamines or esters of simple aliphatic or aromatic acids. Germine is found in Veratrum album, Veratrum dahuricum, Veratrum maackii, Veratrum taliense, Veratrum viride and Zigadenus venenosus. Germine was first documented in 2010 (PMID: 20469637). Based on a literature review a small amount of articles have been published on Germine (PMID: 33767780) (PMID: 32766960) (PMID: 30246539) (PMID: 28876074).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304282200402D          

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M  END

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M  END


  Mrv1652304282200402D          

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    1.6779   -3.1683    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1500   -0.8484    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3511   -0.6477    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8673   -2.0962    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7804   -0.4008    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  1  6  1  0  0  0  0
  5  7  1  0  0  0  0
  8  7  1  6  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
  4 10  1  6  0  0  0
  9 11  1  6  0  0  0
  8 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  1  0  0  0
  7 14  1  0  0  0  0
 13 15  1  0  0  0  0
 16 15  1  1  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 12 18  1  0  0  0  0
 18 19  1  6  0  0  0
 17 20  1  1  0  0  0
 16 21  1  0  0  0  0
 21 22  1  0  0  0  0
 22 23  1  1  0  0  0
 23 24  1  0  0  0  0
 15 24  1  6  0  0  0
 23 25  1  0  0  0  0
 25 26  1  0  0  0  0
 26 27  1  0  0  0  0
 27 28  1  0  0  0  0
 22 28  1  0  0  0  0
 26 29  1  1  0  0  0
 21 30  1  6  0  0  0
 21 31  1  1  0  0  0
 12 32  1  6  0  0  0
  7 33  1  6  0  0  0
  3 33  1  0  0  0  0
  5 34  1  1  0  0  0
  3 35  1  6  0  0  0
  2 36  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0051297

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@H]1CC[C@@H]2N(C1)C[C@H]1[C@@H]3C[C@@]45O[C@@]6(O)[C@@H](C[C@@H](O)[C@H]4[C@]3(O)[C@@H](O)[C@H](O)[C@@H]1[C@]2(C)O)[C@]5(C)CC[C@@H]6O

> <INCHI_IDENTIFIER>
InChI=1S/C27H43NO8/c1-12-4-5-17-24(3,33)19-13(11-28(17)10-12)14-9-25-21(26(14,34)22(32)20(19)31)15(29)8-16-23(25,2)7-6-18(30)27(16,35)36-25/h12-22,29-35H,4-11H2,1-3H3/t12-,13-,14-,15+,16-,17-,18-,19+,20+,21+,22-,23-,24+,25+,26-,27-/m0/s1

> <INCHI_KEY>
RNPABQVCNAUEIY-GUQYYFCISA-N

> <FORMULA>
C27H43NO8

> <MOLECULAR_WEIGHT>
509.64

> <EXACT_MASS>
509.298867349

> <JCHEM_ACCEPTOR_COUNT>
9

> <JCHEM_ATOM_COUNT>
79

> <JCHEM_AVERAGE_POLARIZABILITY>
54.4092551149384

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
7

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1S,2S,6S,9S,10S,11R,12R,13S,14S,15S,16R,18S,19S,22S,23S,25R)-6,10,19-trimethyl-24-oxa-4-azaheptacyclo[12.12.0.0^{2,11}.0^{4,9}.0^{15,25}.0^{18,23}.0^{19,25}]hexacosane-10,12,13,14,16,22,23-heptol

> <ALOGPS_LOGP>
-0.06

> <JCHEM_LOGP>
-1.5064331906666668

> <ALOGPS_LOGS>
-1.63

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
7

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
12.726108818988468

> <JCHEM_PKA_STRONGEST_ACIDIC>
10.91199090815346

> <JCHEM_PKA_STRONGEST_BASIC>
7.971262330874552

> <JCHEM_POLAR_SURFACE_AREA>
154.07999999999998

> <JCHEM_REFRACTIVITY>
127.97839999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.20e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1S,2S,6S,9S,10S,11R,12R,13S,14S,15S,16R,18S,19S,22S,23S,25R)-6,10,19-trimethyl-24-oxa-4-azaheptacyclo[12.12.0.0^{2,11}.0^{4,9}.0^{15,25}.0^{18,23}.0^{19,25}]hexacosane-10,12,13,14,16,22,23-heptol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 28-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   28-APR-22         0                                  
HETATM    1  C   UNK     0      -0.656  -0.016   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -1.814  -1.055   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -1.166  -2.441   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -0.117  -3.277   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.190  -1.981   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.861  -0.401   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       2.026  -2.722   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       2.488  -4.322   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       1.382  -5.377   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -0.041  -4.849   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0       1.693  -6.885   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0       3.989  -4.634   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       4.660  -3.249   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       3.530  -2.169   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       6.196  -3.137   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       7.061  -4.412   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       6.389  -5.798   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       4.853  -5.909   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0       4.182  -7.295   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0       7.254  -7.072   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0       8.597  -4.300   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       9.268  -2.914   0.000  0.00  0.00           C+0
HETATM   23  N   UNK     0       8.404  -1.640   0.000  0.00  0.00           N+0
HETATM   24  C   UNK     0       6.868  -1.751   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       9.075  -0.254   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      10.611  -0.143   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      11.476  -1.417   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      10.804  -2.803   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      11.283   1.243   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       8.762  -5.831   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0       9.958  -5.020   0.000  0.00  0.00           O+0
HETATM   32  O   UNK     0       3.132  -5.914   0.000  0.00  0.00           O+0
HETATM   33  O   UNK     0       0.280  -1.584   0.000  0.00  0.00           O+0
HETATM   34  C   UNK     0       2.522  -1.209   0.000  0.00  0.00           C+0
HETATM   35  O   UNK     0      -1.619  -3.913   0.000  0.00  0.00           O+0
HETATM   36  O   UNK     0      -3.323  -0.748   0.000  0.00  0.00           O+0
CONECT    1    2    6                                                       
CONECT    2    1    3   36                                                  
CONECT    3    2    4   33   35                                             
CONECT    4    3    5   10                                                  
CONECT    5    4    6    7   34                                             
CONECT    6    5    1                                                       
CONECT    7    5    8   14   33                                             
CONECT    8    7    9   12                                                  
CONECT    9    8   10   11                                                  
CONECT   10    9    4                                                       
CONECT   11    9                                                            
CONECT   12    8   13   18   32                                             
CONECT   13   12   14   15                                                  
CONECT   14   13    7                                                       
CONECT   15   13   16   24                                                  
CONECT   16   15   17   21                                                  
CONECT   17   16   18   20                                                  
CONECT   18   17   12   19                                                  
CONECT   19   18                                                            
CONECT   20   17                                                            
CONECT   21   16   22   30   31                                             
CONECT   22   21   23   28                                                  
CONECT   23   22   24   25                                                  
CONECT   24   23   15                                                       
CONECT   25   23   26                                                       
CONECT   26   25   27   29                                                  
CONECT   27   26   28                                                       
CONECT   28   27   22                                                       
CONECT   29   26                                                            
CONECT   30   21                                                            
CONECT   31   21                                                            
CONECT   32   12                                                            
CONECT   33    7    3                                                       
CONECT   34    5                                                            
CONECT   35    3                                                            
CONECT   36    2                                                            
MASTER        0    0    0    0    0    0    0    0   36    0   84    0
END

View in JSmol

Synonyms

Value	Source
Germabenzene	MeSH
Germine hydrochloride	MeSH

Chemical Formula

C₂₇H₄₃NO₈

Average Mass

509.6400 Da

Monoisotopic Mass

509.29887 Da

IUPAC Name

(1S,2S,6S,9S,10S,11R,12R,13S,14S,15S,16R,18S,19S,22S,23S,25R)-6,10,19-trimethyl-24-oxa-4-azaheptacyclo[12.12.0.0^{2,11}.0^{4,9}.0^{15,25}.0^{18,23}.0^{19,25}]hexacosane-10,12,13,14,16,22,23-heptol

Traditional Name

(1S,2S,6S,9S,10S,11R,12R,13S,14S,15S,16R,18S,19S,22S,23S,25R)-6,10,19-trimethyl-24-oxa-4-azaheptacyclo[12.12.0.0^{2,11}.0^{4,9}.0^{15,25}.0^{18,23}.0^{19,25}]hexacosane-10,12,13,14,16,22,23-heptol

CAS Registry Number

Not Available

SMILES

C[C@H]1CC[C@@H]2N(C1)C[C@H]1[C@@H]3C[C@@]45O[C@@]6(O)[C@@H](C[C@@H](O)[C@H]4[C@]3(O)[C@@H](O)[C@H](O)[C@@H]1[C@]2(C)O)[C@]5(C)CC[C@@H]6O

InChI Identifier

InChI=1S/C27H43NO8/c1-12-4-5-17-24(3,33)19-13(11-28(17)10-12)14-9-25-21(26(14,34)22(32)20(19)31)15(29)8-16-23(25,2)7-6-18(30)27(16,35)36-25/h12-22,29-35H,4-11H2,1-3H3/t12-,13-,14-,15+,16-,17-,18-,19+,20+,21+,22-,23-,24+,25+,26-,27-/m0/s1

InChI Key

RNPABQVCNAUEIY-GUQYYFCISA-N

Experimental Spectra

Not Available

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 25 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Veratrum album	LOTUS Database	35616633
Veratrum dahuricum	LOTUS Database	35616633
Veratrum maackii	LOTUS Database	35616633
Veratrum taliense	Plant	KNApSAcK
Veratrum viride	Plant	KNApSAcK
Zigadenus venenosus	Plant	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as cerveratrum-type alkaloids. These are steroidal alkaloids containing the cevane (23-methyl-4- azahexacyclo[12.11.0.0^{2,11}.0^{4,9}.0^{15,24}.0^{18,23}]Pentacosane) moiety, which is a six ring system. Cerveratrum alkaloids have 7-9 oxygen atoms and occur as free alkamines or esters of simple aliphatic or aromatic acids.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Steroids and steroid derivatives

Sub Class

Steroidal alkaloids

Direct Parent

Cerveratrum-type alkaloids

Alternative Parents

Substituents

Cerveratrum-type alkaloid
Azasteroid
Quinolizidine
Alkaloid or derivatives
Oxepane
Piperidine
Cyclic alcohol
Tertiary alcohol
Tetrahydrofuran
Tertiary amine
Secondary alcohol
Tertiary aliphatic amine
1,2-aminoalcohol
Hemiacetal
Azacycle
Organoheterocyclic compound
Oxacycle
Polyol
Alcohol
Organonitrogen compound
Organooxygen compound
Organopnictogen compound
Organic oxygen compound
Organic nitrogen compound
Amine
Hydrocarbon derivative
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic heteropolycyclic compounds

External Descriptors

alkaloid (CHEBI:5338 )
Steroidal alkaloids (C10807 )

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	-0.06	ALOGPS
logP	-1.5	ChemAxon
logS	-1.6	ALOGPS
pKa (Strongest Acidic)	10.91	ChemAxon
pKa (Strongest Basic)	7.97	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	9	ChemAxon
Hydrogen Donor Count	7	ChemAxon
Polar Surface Area	154.08 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	127.98 m³·mol⁻¹	ChemAxon
Polarizability	54.41 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	No	ChemAxon

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

C00002250

Chemspider ID

391279

KEGG Compound ID

C10807

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Germabenzene

METLIN ID

Not Available

PubChem Compound

442976

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Pop L, Suciu I, Ionescu O, Bacalbasa N, Ionescu P: The role of novel poly (ADP-ribose) inhibitors in the treatment of locally advanced and metastatic Her-2/neu negative breast cancer with inherited germline BRCA1/2 mutations. A review of the literature. J Med Life. 2021 Jan-Mar;14(1):17-20. doi: 10.25122/jml-2020-0132. [PubMed:33767780 ]
Suzuki K, Takazawa T, Saito S: History of the development of antagonists for neuromuscular blocking agents. J Anesth. 2020 Oct;34(5):723-728. doi: 10.1007/s00540-020-02836-1. Epub 2020 Aug 7. [PubMed:32766960 ]
Xue XS, Levandowski BJ, He CQ, Houk KN: Origins of Selectivities in the Stork Diels-Alder Cycloaddition for the Synthesis of (+/-)-4-Methylenegermine. Org Lett. 2018 Oct 5;20(19):6108-6111. doi: 10.1021/acs.orglett.8b02548. Epub 2018 Sep 24. [PubMed:30246539 ]
Stork G, Yamashita A, Hanson RM, Phan L, Phillips E, Dube D, Bos PH, Clark AJ, Gough M, Greenlee ML, Jiang Y, Jones K, Kitamura M, Leonard J, Liu T, Parsons PJ, Venkatesan AM: Synthetic Study toward Total Synthesis of (+/-)-Germine: Synthesis of (+/-)-4-Methylenegermine. Org Lett. 2017 Oct 6;19(19):5150-5153. doi: 10.1021/acs.orglett.7b02434. Epub 2017 Sep 6. [PubMed:28876074 ]
Christov V, Mikhova B, Ivanova A, Serly J, Molnar J, Selenge D, Solongo A, Kostova N, Gerelt-Od Y, Dimitrov D: Steroidal alkaloids of Veratrum lobelianum Bernh. and Veratrum nigrum L. Z Naturforsch C J Biosci. 2010 Mar-Apr;65(3-4):195-200. doi: 10.1515/znc-2010-3-405. [PubMed:20469637 ]

Showing NP-Card for Germine (NP0051297)

MOL for NP0051297 (Germine)

3D MOL for NP0051297 (Germine)

3D SDF for NP0051297 (Germine)

3D-SDF for NP0051297 (Germine)

PDB for NP0051297 (Germine)

3D PDB for NP0051297 (Germine)

SMILES for NP0051297 (Germine)

INCHI for NP0051297 (Germine)

Structure for NP0051297 (Germine)

3D Structure for NP0051297 (Germine)