NP-MRD: Showing NP-Card for eudistomin c (NP0288777)

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Record Information

Version

2.0

Created at

2022-09-09 18:38:23 UTC

Updated at

2022-09-09 18:38:23 UTC

NP-MRD ID

NP0288777

Secondary Accession Numbers

None

Natural Product Identification

Common Name

eudistomin c

Description

Eudistomin C belongs to the class of organic compounds known as beta carbolines. Beta carbolines are compounds containing a 9H-pyrido[3,4-b]indole moiety. Eudistomin C is a secondary metabolite. Secondary metabolites are metabolically or physiologically non-essential metabolites that may serve a role as defense or signalling molecules. In some cases they are simply molecules that arise from the incomplete metabolism of other secondary metabolites. eudistomin c was first documented in 2005 (PMID: 16248638). Based on a literature review a small amount of articles have been published on eudistomin C (PMID: 27304596) (PMID: 18498172).

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 37 40  0  0  0  0  0  0  0  0999 V2000
   -1.8649   -2.1334   -0.6288 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3659   -1.1612    0.3200 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.6743   -0.6569   -0.2563 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5262    0.4988    0.8211 S   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7557    2.1405    0.5315 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4316    2.0083    0.8580 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7468    1.1876   -0.0080 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6485    1.9954   -0.4778 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4757    1.9200    0.5706 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9692    0.5277    0.4262 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0225   -0.4633    0.4375 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7023   -1.6096    0.2864 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.0277   -1.3767    0.1820 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1384   -2.1854    0.0174 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3945   -1.6474   -0.0570 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9362   -2.7504   -0.2840 Br  0  0  0  0  0  0  0  0  0  0  0  0
    4.5799   -0.2902    0.0305 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8606    0.2509   -0.0459 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5005    0.5245    0.1927 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2080   -0.0136    0.2704 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3787   -0.0608    0.6057 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.2743   -2.0321   -1.5764 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9687   -3.1222   -0.2899 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6272   -1.7281    1.2378 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3244   -1.5558   -0.3643 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4712   -0.2161   -1.2615 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9474    2.4869   -0.4996 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2162    2.8476    1.2185 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9342    3.0527   -0.5238 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2762    1.7000   -1.4734 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0225    2.0097    1.5625 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2438    2.6723    0.3919 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2989   -2.5455    0.2520 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9711   -3.2500   -0.0492 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.0156    1.2343    0.0155 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5877    1.6076    0.2681 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4779    0.1339    1.7209 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  2  0
 11 12  1  0
 12 13  1  0
 13 14  2  0
 14 15  1  0
 15 16  1  0
 15 17  2  0
 17 18  1  0
 17 19  1  0
 19 20  2  0
 11 21  1  0
 21  2  1  0
 21  7  1  0
 20 10  1  0
 20 13  1  0
  1 22  1  0
  1 23  1  0
  2 24  1  1
  3 25  1  0
  3 26  1  0
  5 27  1  0
  5 28  1  0
  8 29  1  0
  8 30  1  0
  9 31  1  0
  9 32  1  0
 12 33  1  0
 14 34  1  0
 18 35  1  0
 19 36  1  0
 21 37  1  1
M  END


  Mrv1652309092220382D          

 21 24  0  0  1  0            999 V2000
    1.9646   -0.9751    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4498   -0.3304    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.6456   -0.5145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0003   -0.0005    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0003    0.8245    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6444    1.3392    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4489    1.1562    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.9132    1.8381    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7359    1.7769    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0943    1.0339    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6300    0.3519    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1351   -0.3004    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.9116   -0.0216    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6383   -0.4121    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3398    0.0220    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0666   -0.3685    0.0000 Br  0  0  0  0  0  0  0  0  0  0  0  0
    5.3146    0.8466    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0162    1.2807    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.5879    1.2371    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8864    0.8030    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8073    0.4131    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
  2  1  1  6  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
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  2  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  2  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 15 17  2  0  0  0  0
 17 18  1  0  0  0  0
 17 19  1  0  0  0  0
 19 20  2  0  0  0  0
 10 20  1  0  0  0  0
 13 20  1  0  0  0  0
 21 11  1  6  0  0  0
  2 21  1  0  0  0  0
  7 21  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0288777

> <DATABASE_NAME>
NP-MRD

> <SMILES>
N[C@@H]1CSCON2CCC3=C(NC4=CC(Br)=C(O)C=C34)[C@H]12

> <INCHI_IDENTIFIER>
InChI=1S/C14H16BrN3O2S/c15-9-4-11-8(3-12(9)19)7-1-2-18-14(13(7)17-11)10(16)5-21-6-20-18/h3-4,10,14,17,19H,1-2,5-6,16H2/t10-,14+/m1/s1

> <INCHI_KEY>
XHYJPORPMFTSBP-YGRLFVJLSA-N

> <FORMULA>
C14H16BrN3O2S

> <MOLECULAR_WEIGHT>
370.27

> <EXACT_MASS>
369.014661

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
37

> <JCHEM_AVERAGE_POLARIZABILITY>
34.83571690507155

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(2S,3S)-3-amino-15-bromo-7-oxa-5-thia-8,18-diazatetracyclo[9.7.0.0^{2,8}.0^{12,17}]octadeca-1(11),12,14,16-tetraen-14-ol

> <JCHEM_LOGP>
0.7319635298937637

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
17.05859098120765

> <JCHEM_PKA_STRONGEST_ACIDIC>
7.649465912854467

> <JCHEM_PKA_STRONGEST_BASIC>
8.825013044621349

> <JCHEM_POLAR_SURFACE_AREA>
74.51

> <JCHEM_REFRACTIVITY>
87.0212

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(2S,3S)-3-amino-15-bromo-7-oxa-5-thia-8,18-diazatetracyclo[9.7.0.0^{2,8}.0^{12,17}]octadeca-1(11),12,14,16-tetraen-14-ol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 09-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   09-SEP-22         0                                  
HETATM    1  N   UNK     0       3.667  -1.820   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0       2.706  -0.617   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.205  -0.960   0.000  0.00  0.00           C+0
HETATM    4  S   UNK     0       0.000  -0.001   0.000  0.00  0.00           S+0
HETATM    5  C   UNK     0      -0.000   1.539   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       1.203   2.500   0.000  0.00  0.00           O+0
HETATM    7  N   UNK     0       2.705   2.158   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0       3.571   3.431   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       5.107   3.317   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       5.776   1.930   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       4.909   0.657   0.000  0.00  0.00           C+0
HETATM   12  N   UNK     0       5.852  -0.561   0.000  0.00  0.00           N+0
HETATM   13  C   UNK     0       7.302  -0.040   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       8.658  -0.769   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       9.968   0.041   0.000  0.00  0.00           C+0
HETATM   16 Br   UNK     0      11.324  -0.688   0.000  0.00  0.00          Br+0
HETATM   17  C   UNK     0       9.921   1.580   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0      11.230   2.391   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0       8.564   2.309   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       7.255   1.499   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       3.374   0.771   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3   21                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8   21                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11   20                                                  
CONECT   11   10   12   21                                                  
CONECT   12   11   13                                                       
CONECT   13   12   14   20                                                  
CONECT   14   13   15                                                       
CONECT   15   14   16   17                                                  
CONECT   16   15                                                            
CONECT   17   15   18   19                                                  
CONECT   18   17                                                            
CONECT   19   17   20                                                       
CONECT   20   19   10   13                                                  
CONECT   21   11    2    7                                                  
MASTER        0    0    0    0    0    0    0    0   21    0   48    0
END

View in JSmol

Synonyms

Value	Source
(-)-Eudistomin C	ChEBI
(-)-Eudistomine C	ChEBI
Eudistomine C	ChEBI

Chemical Formula

C₁₄H₁₆BrN₃O₂S

Average Mass

370.2700 Da

Monoisotopic Mass

369.01466 Da

IUPAC Name

(2S,3S)-3-amino-15-bromo-7-oxa-5-thia-8,18-diazatetracyclo[9.7.0.0^{2,8}.0^{12,17}]octadeca-1(11),12,14,16-tetraen-14-ol

Traditional Name

(2S,3S)-3-amino-15-bromo-7-oxa-5-thia-8,18-diazatetracyclo[9.7.0.0^{2,8}.0^{12,17}]octadeca-1(11),12,14,16-tetraen-14-ol

CAS Registry Number

Not Available

SMILES

N[C@@H]1CSCON2CCC3=C(NC4=CC(Br)=C(O)C=C34)[C@H]12

InChI Identifier

InChI=1S/C14H16BrN3O2S/c15-9-4-11-8(3-12(9)19)7-1-2-18-14(13(7)17-11)10(16)5-21-6-20-18/h3-4,10,14,17,19H,1-2,5-6,16H2/t10-,14+/m1/s1

InChI Key

XHYJPORPMFTSBP-YGRLFVJLSA-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, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Not Available

Species

Species of Origin

Not Available

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as beta carbolines. Beta carbolines are compounds containing a 9H-pyrido[3,4-b]indole moiety.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Indoles and derivatives

Sub Class

Pyridoindoles

Direct Parent

Beta carbolines

Alternative Parents

Substituents

Beta-carboline
Hydroxyindole
3-alkylindole
Indole
2-bromophenol
1-hydroxy-2-unsubstituted benzenoid
Aralkylamine
Aryl bromide
Aryl halide
Benzenoid
Heteroaromatic compound
Pyrrole
Oxacycle
Azacycle
N-organohydroxylamine
Organooxygen compound
Organonitrogen compound
Organobromide
Organohalogen compound
Amine
Primary aliphatic amine
Hydrocarbon derivative
Organopnictogen compound
Organic oxygen compound
Primary amine
Organic nitrogen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

beta-carbolines (CHEBI:80955 )

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	0.73	ChemAxon
pKa (Strongest Acidic)	7.65	ChemAxon
pKa (Strongest Basic)	8.83	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	74.51 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	87.02 m³·mol⁻¹	ChemAxon
Polarizability	34.84 Å³	ChemAxon
Number of Rings	4	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	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

Not Available

Chemspider ID

160734

KEGG Compound ID

C17167

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

184887

PDB ID

Not Available

ChEBI ID

80955

Good Scents ID

Not Available

References

General References

Ota Y, Chinen T, Yoshida K, Kudo S, Nagumo Y, Shiwa Y, Yamada R, Umihara H, Iwasaki K, Masumoto H, Yokoshima S, Yoshikawa H, Fukuyama T, Kobayashi J, Usui T: Eudistomin C, an Antitumor and Antiviral Natural Product, Targets 40S Ribosome and Inhibits Protein Translation. Chembiochem. 2016 Sep 2;17(17):1616-20. doi: 10.1002/cbic.201600075. Epub 2016 Jul 22. [PubMed:27304596 ]
Yamagishi H, Matsumoto K, Iwasaki K, Miyazaki T, Yokoshima S, Tokuyama H, Fukuyama T: Synthesis of eudistomin C and E: improved preparation of the indole unit. Org Lett. 2008 Jun 19;10(12):2369-72. doi: 10.1021/ol800527p. Epub 2008 May 23. [PubMed:18498172 ]
Yamashita T, Kawai N, Tokuyama H, Fukuyama T: Stereocontrolled total synthesis of (-)-eudistomin C. J Am Chem Soc. 2005 Nov 2;127(43):15038-9. doi: 10.1021/ja055832h. [PubMed:16248638 ]
LOTUS database [Link]

Showing NP-Card for eudistomin c (NP0288777)

MOL for NP0288777 (eudistomin c)

3D MOL for NP0288777 (eudistomin c)

3D SDF for NP0288777 (eudistomin c)

3D-SDF for NP0288777 (eudistomin c)

PDB for NP0288777 (eudistomin c)

3D PDB for NP0288777 (eudistomin c)

SMILES for NP0288777 (eudistomin c)

INCHI for NP0288777 (eudistomin c)

Structure for NP0288777 (eudistomin c)

3D Structure for NP0288777 (eudistomin c)