NP-MRD: Showing NP-Card for 3-[(6-hydroxy-1h-indol-3-yl)methyl]-6-(3-methylbut-2-en-1-yl)-3h-1,4-benzodiazepine-2,5,9-triol (NP0210721)

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Record Information

Version

2.0

Created at

2022-09-05 08:39:55 UTC

Updated at

2022-09-05 08:39:55 UTC

NP-MRD ID

NP0210721

Secondary Accession Numbers

None

Natural Product Identification

Common Name

3-[(6-hydroxy-1h-indol-3-yl)methyl]-6-(3-methylbut-2-en-1-yl)-3h-1,4-benzodiazepine-2,5,9-triol

Description

3-[(6-Hydroxy-1H-indol-3-yl)methyl]-6-(3-methylbut-2-en-1-yl)-3H-1,4-benzodiazepine-2,5,9-triol belongs to the class of organic compounds known as 1,4-benzodiazepines. These are organic compounds containing a benzene ring fused to a 1,4-azepine. Based on a literature review very few articles have been published on 3-[(6-hydroxy-1H-indol-3-yl)methyl]-6-(3-methylbut-2-en-1-yl)-3H-1,4-benzodiazepine-2,5,9-triol.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309052210392D          

 30 33  0  0  0  0            999 V2000
   -4.4233    4.0050    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6387    3.7500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0256    4.3021    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4672    2.9430    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6826    2.6881    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5110    1.8811    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1241    1.3291    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9526    0.5221    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1680    0.2672    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9965   -0.5398    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5549    0.8192    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7264    1.6262    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2024    2.2634    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5492    3.0120    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3775    2.2511    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.1271    1.5985    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9341    1.7700    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1890    2.5546    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7041    3.2221    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1890    3.8895    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.9737    3.6346    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6881    4.0471    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4026    3.6346    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1171    4.0471    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4026    2.8096    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6881    2.3971    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9737    2.8096    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0685    0.7970    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5688    0.2730    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8170    0.4502    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
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 28 29  1  0  0  0  0
 28 30  2  0  0  0  0
 11 30  1  0  0  0  0
M  END

     RDKit          3D

 53 56  0  0  0  0  0  0  0  0999 V2000
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    3.5351    1.6548    0.9086 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7496    1.7425    0.3682 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.2180    0.4944    0.1004 C   0  0  0  0  0  0  0  0  0  0  0  0
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    6.6379   -1.2833   -0.6214 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.8354   -1.7072   -1.1796 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.7042   -2.2212   -0.2461 C   0  0  0  0  0  0  0  0  0  0  0  0
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 29 53  1  0
M  END


  Mrv1652309052210392D          

 30 33  0  0  0  0            999 V2000
   -4.4233    4.0050    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6387    3.7500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0256    4.3021    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4672    2.9430    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6826    2.6881    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5110    1.8811    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1241    1.3291    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9526    0.5221    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1680    0.2672    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9965   -0.5398    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5549    0.8192    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7264    1.6262    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2024    2.2634    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5492    3.0120    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3775    2.2511    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.1271    1.5985    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9341    1.7700    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    0.7041    3.2221    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1890    3.8895    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.9737    3.6346    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6881    4.0471    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4026    3.6346    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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 28 29  1  0  0  0  0
 28 30  2  0  0  0  0
 11 30  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0210721

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(C)=CCC1=CC=C(O)C2=C1C(O)=NC(CC1=CNC3=CC(O)=CC=C13)C(O)=N2

> <INCHI_IDENTIFIER>
InChI=1S/C23H23N3O4/c1-12(2)3-4-13-5-8-19(28)21-20(13)23(30)25-18(22(29)26-21)9-14-11-24-17-10-15(27)6-7-16(14)17/h3,5-8,10-11,18,24,27-28H,4,9H2,1-2H3,(H,25,30)(H,26,29)

> <INCHI_KEY>
WTCPFXAMIWMDMP-UHFFFAOYSA-N

> <FORMULA>
C23H23N3O4

> <MOLECULAR_WEIGHT>
405.454

> <EXACT_MASS>
405.168856233

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
53

> <JCHEM_AVERAGE_POLARIZABILITY>
42.88782282441176

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
3-[(6-hydroxy-1H-indol-3-yl)methyl]-6-(3-methylbut-2-en-1-yl)-3H-1,4-benzodiazepine-2,5,9-triol

> <JCHEM_LOGP>
3.0379024862826887

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
6.5921612049238005

> <JCHEM_PKA_STRONGEST_ACIDIC>
0.5173363671113207

> <JCHEM_PKA_STRONGEST_BASIC>
8.15106208226315

> <JCHEM_POLAR_SURFACE_AREA>
121.43

> <JCHEM_REFRACTIVITY>
118.01780000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
3-[(6-hydroxy-1H-indol-3-yl)methyl]-6-(3-methylbut-2-en-1-yl)-3H-1,4-benzodiazepine-2,5,9-triol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 05-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   05-SEP-22         0                                  
HETATM    1  C   UNK     0      -8.257   7.476   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -6.792   7.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -5.648   8.031   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -6.472   5.494   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -5.007   5.018   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -4.687   3.511   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -5.832   2.481   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -5.512   0.975   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -4.047   0.499   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      -3.727  -1.008   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0      -2.902   1.529   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -3.223   3.036   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -2.245   4.225   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0      -2.892   5.622   0.000  0.00  0.00           O+0
HETATM   15  N   UNK     0      -0.705   4.202   0.000  0.00  0.00           N+0
HETATM   16  C   UNK     0       0.237   2.984   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       1.744   3.304   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       2.220   4.769   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       1.314   6.015   0.000  0.00  0.00           C+0
HETATM   20  N   UNK     0       2.220   7.260   0.000  0.00  0.00           N+0
HETATM   21  C   UNK     0       3.684   6.785   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       5.018   7.555   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       6.352   6.785   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0       7.685   7.555   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0       6.352   5.245   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       5.018   4.475   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       3.684   5.245   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      -0.128   1.488   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0       1.062   0.510   0.000  0.00  0.00           O+0
HETATM   30  N   UNK     0      -1.525   0.840   0.000  0.00  0.00           N+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7   12                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9   12   30                                                  
CONECT   12   11    6   13                                                  
CONECT   13   12   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13   16                                                       
CONECT   16   15   17   28                                                  
CONECT   17   16   18                                                       
CONECT   18   17   19   27                                                  
CONECT   19   18   20                                                       
CONECT   20   19   21                                                       
CONECT   21   20   22   27                                                  
CONECT   22   21   23                                                       
CONECT   23   22   24   25                                                  
CONECT   24   23                                                            
CONECT   25   23   26                                                       
CONECT   26   25   27                                                       
CONECT   27   26   18   21                                                  
CONECT   28   16   29   30                                                  
CONECT   29   28                                                            
CONECT   30   28   11                                                       
MASTER        0    0    0    0    0    0    0    0   30    0   66    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₃H₂₃N₃O₄

Average Mass

405.4540 Da

Monoisotopic Mass

405.16886 Da

IUPAC Name

3-[(6-hydroxy-1H-indol-3-yl)methyl]-6-(3-methylbut-2-en-1-yl)-3H-1,4-benzodiazepine-2,5,9-triol

Traditional Name

3-[(6-hydroxy-1H-indol-3-yl)methyl]-6-(3-methylbut-2-en-1-yl)-3H-1,4-benzodiazepine-2,5,9-triol

CAS Registry Number

Not Available

SMILES

CC(C)=CCC1=CC=C(O)C2=C1C(O)=NC(CC1=CNC3=CC(O)=CC=C13)C(O)=N2

InChI Identifier

InChI=1S/C23H23N3O4/c1-12(2)3-4-13-5-8-19(28)21-20(13)23(30)25-18(22(29)26-21)9-14-11-24-17-10-15(27)6-7-16(14)17/h3,5-8,10-11,18,24,27-28H,4,9H2,1-2H3,(H,25,30)(H,26,29)

InChI Key

WTCPFXAMIWMDMP-UHFFFAOYSA-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 1,4-benzodiazepines. These are organic compounds containing a benzene ring fused to a 1,4-azepine.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Benzodiazepines

Sub Class

1,4-benzodiazepines

Direct Parent

1,4-benzodiazepines

Alternative Parents

Substituents

1,4-benzodiazepine
Alpha-amino acid or derivatives
3-alkylindole
Hydroxyindole
Indole
Indole or derivatives
1-hydroxy-2-unsubstituted benzenoid
Substituted pyrrole
Benzenoid
Pyrrole
Heteroaromatic compound
Vinylogous amide
Secondary carboxylic acid amide
Lactam
Carboxamide group
Carboxylic acid derivative
Azacycle
Organopnictogen compound
Hydrocarbon derivative
Organic oxide
Organooxygen compound
Organonitrogen compound
Organic nitrogen compound
Carbonyl group
Organic oxygen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

Not Available

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	3.04	ChemAxon
pKa (Strongest Acidic)	0.52	ChemAxon
pKa (Strongest Basic)	8.15	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	121.43 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	118.02 m³·mol⁻¹	ChemAxon
Polarizability	42.89 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

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

162961581

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for 3-[(6-hydroxy-1h-indol-3-yl)methyl]-6-(3-methylbut-2-en-1-yl)-3h-1,4-benzodiazepine-2,5,9-triol (NP0210721)

MOL for NP0210721 (3-[(6-hydroxy-1h-indol-3-yl)methyl]-6-(3-methylbut-2-en-1-yl)-3h-1,4-benzodiazepine-2,5,9-triol)

3D MOL for NP0210721 (3-[(6-hydroxy-1h-indol-3-yl)methyl]-6-(3-methylbut-2-en-1-yl)-3h-1,4-benzodiazepine-2,5,9-triol)

3D SDF for NP0210721 (3-[(6-hydroxy-1h-indol-3-yl)methyl]-6-(3-methylbut-2-en-1-yl)-3h-1,4-benzodiazepine-2,5,9-triol)

3D-SDF for NP0210721 (3-[(6-hydroxy-1h-indol-3-yl)methyl]-6-(3-methylbut-2-en-1-yl)-3h-1,4-benzodiazepine-2,5,9-triol)

PDB for NP0210721 (3-[(6-hydroxy-1h-indol-3-yl)methyl]-6-(3-methylbut-2-en-1-yl)-3h-1,4-benzodiazepine-2,5,9-triol)

3D PDB for NP0210721 (3-[(6-hydroxy-1h-indol-3-yl)methyl]-6-(3-methylbut-2-en-1-yl)-3h-1,4-benzodiazepine-2,5,9-triol)

SMILES for NP0210721 (3-[(6-hydroxy-1h-indol-3-yl)methyl]-6-(3-methylbut-2-en-1-yl)-3h-1,4-benzodiazepine-2,5,9-triol)

INCHI for NP0210721 (3-[(6-hydroxy-1h-indol-3-yl)methyl]-6-(3-methylbut-2-en-1-yl)-3h-1,4-benzodiazepine-2,5,9-triol)

Structure for NP0210721 (3-[(6-hydroxy-1h-indol-3-yl)methyl]-6-(3-methylbut-2-en-1-yl)-3h-1,4-benzodiazepine-2,5,9-triol)

3D Structure for NP0210721 (3-[(6-hydroxy-1h-indol-3-yl)methyl]-6-(3-methylbut-2-en-1-yl)-3h-1,4-benzodiazepine-2,5,9-triol)