NP-MRD: Showing NP-Card for (R)-3,4-dihydro-3-(1H-indol-3-ylmethyl)-4-methyl-1H-1,4-benzodiazepine-2,5-dione (NP0044126)

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Record Information

Version

1.0

Created at

2021-11-12 23:51:29 UTC

Updated at

2021-11-26 17:45:43 UTC

NP-MRD ID

NP0044126

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(R)-3,4-dihydro-3-(1H-indol-3-ylmethyl)-4-methyl-1H-1,4-benzodiazepine-2,5-dione

Description

It was first documented in 2018 (PMID: 30018423).

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 41 44  0  0  0  0  0  0  0  0999 V2000
   -0.5362   -1.1112    2.8606 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0117   -0.8904    1.4725 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3807   -1.1693    1.2654 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8695   -2.1352    1.9485 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3442   -0.5299    0.3898 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6419   -0.7816    0.7002 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6473   -0.2431   -0.0481 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3811    0.5652   -1.1316 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0749    0.8339   -1.4643 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0623    0.2936   -0.7140 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7649    0.6544   -1.1668 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5364    0.1093   -0.7338 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3362    0.0999   -1.6779 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0384   -0.4392    0.5304 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.8877    0.6124    1.1296 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8936    1.0702    0.1383 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9174    2.2406   -0.5977 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0146    2.2673   -1.3938 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.7155    1.1392   -1.1990 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8912    0.6406   -1.7265 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4017   -0.5809   -1.3372 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7257   -1.3386   -0.3912 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5636   -0.8161    0.1118 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0304    0.3852   -0.2491 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5502   -0.1932    3.4493 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4356   -1.6434    2.8309 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2541   -1.8185    3.3345 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8327   -1.4267    1.5677 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.6690   -0.4760    0.2395 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2174    0.9753   -1.7043 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8827    1.4660   -2.3143 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7663    1.4086   -1.8992 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6574   -1.2898    0.2393 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3978    0.1940    2.0329 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3127    1.4930    1.4779 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1675    3.0235   -0.5463 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3086    3.0152   -2.0622 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4361    1.2197   -2.4694 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.3150   -1.0129   -1.7218 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0541   -2.2944   -0.0362 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9995   -1.3861    0.8655 H   0  0  0  0  0  0  0  0  0  0  0  0
  4  3  2  0
  3  2  1  0
  2  1  1  0
  2 14  1  0
 14 15  1  0
 15 16  1  0
 16 17  2  0
 17 18  1  0
 18 19  1  0
 19 20  2  0
 20 21  1  0
 21 22  2  0
 22 23  1  0
 23 24  2  0
  3  5  1  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  2  0
  5 10  2  0
 10 11  1  0
 11 12  1  0
 12 13  2  0
 12 14  1  0
 24 16  1  0
 24 19  1  0
 10  9  1  0
  1 25  1  0
  1 26  1  0
  1 27  1  0
 14 33  1  6
 15 34  1  0
 15 35  1  0
 17 36  1  0
 18 37  1  0
 20 38  1  0
 21 39  1  0
 22 40  1  0
 23 41  1  0
  6 28  1  0
  7 29  1  0
  8 30  1  0
  9 31  1  0
 11 32  1  0
M  END


  Mrv1652311132100512D          

 24 27  0  0  1  0            999 V2000
    3.4479    1.4620    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6315    0.6577    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4358    0.4742    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.9502    1.1192    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7938   -0.2691    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.6188   -0.2691    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0313   -0.9836    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6957   -1.7373    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.3088   -2.2893    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    7.0233   -1.8768    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.8079   -2.1318    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.4210   -1.5797    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.2495   -0.7728    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.4648   -0.5178    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.8518   -1.0699    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9865    0.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2720    0.5559    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5575    0.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5575   -0.6816    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2720   -1.0941    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9865   -0.6816    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6315   -1.1960    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.4358   -1.0124    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9502   -1.6575    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  3  5  1  0  0  0  0
  5  6  1  6  0  0  0
  6  7  1  0  0  0  0
  7  8  2  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  2  0  0  0  0
 13 14  1  0  0  0  0
 14 15  2  0  0  0  0
  7 15  1  0  0  0  0
 10 15  1  0  0  0  0
  2 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  2  0  0  0  0
 18 19  1  0  0  0  0
 19 20  2  0  0  0  0
 16 21  2  0  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
 22 23  1  0  0  0  0
  5 23  1  0  0  0  0
 23 24  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0044126

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CN1[C@H](CC2=CNC3=CC=CC=C23)C(=O)NC2=C(C=CC=C2)C1=O

> <INCHI_IDENTIFIER>
InChI=1S/C19H17N3O2/c1-22-17(10-12-11-20-15-8-4-2-6-13(12)15)18(23)21-16-9-5-3-7-14(16)19(22)24/h2-9,11,17,20H,10H2,1H3,(H,21,23)/t17-/m1/s1

> <INCHI_KEY>
QYBGEUDXQJVALS-QGZVFWFLSA-N

> <FORMULA>
C19H17N3O2

> <MOLECULAR_WEIGHT>
319.364

> <EXACT_MASS>
319.132076799

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
41

> <JCHEM_AVERAGE_POLARIZABILITY>
32.14808935527932

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(3R)-3-[(1H-indol-3-yl)methyl]-4-methyl-2,3,4,5-tetrahydro-1H-1,4-benzodiazepine-2,5-dione

> <ALOGPS_LOGP>
2.80

> <JCHEM_LOGP>
3.1841302346666662

> <ALOGPS_LOGS>
-3.60

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
16.15474635834842

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.012271488180106

> <JCHEM_PKA_STRONGEST_BASIC>
-1.79357278358615

> <JCHEM_POLAR_SURFACE_AREA>
65.2

> <JCHEM_REFRACTIVITY>
93.43310000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
8.10e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(3R)-3-(1H-indol-3-ylmethyl)-4-methyl-1,3-dihydro-1,4-benzodiazepine-2,5-dione

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 13-NOV-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   13-NOV-21         0                                  
HETATM    1  O   UNK     0       6.436   2.729   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       6.779   1.228   0.000  0.00  0.00           C+0
HETATM    3  N   UNK     0       8.280   0.885   0.000  0.00  0.00           N+0
HETATM    4  C   UNK     0       9.240   2.089   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       8.948  -0.502   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      10.488  -0.502   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      11.258  -1.836   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      10.632  -3.243   0.000  0.00  0.00           C+0
HETATM    9  N   UNK     0      11.776  -4.273   0.000  0.00  0.00           N+0
HETATM   10  C   UNK     0      13.110  -3.503   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      14.575  -3.979   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      15.719  -2.949   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      15.399  -1.442   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      13.934  -0.967   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      12.790  -1.997   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       5.575   0.268   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       4.241   1.038   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       2.907   0.268   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       2.907  -1.272   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       4.241  -2.042   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       5.575  -1.272   0.000  0.00  0.00           C+0
HETATM   22  N   UNK     0       6.779  -2.233   0.000  0.00  0.00           N+0
HETATM   23  C   UNK     0       8.280  -1.890   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0       9.240  -3.094   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   16                                                  
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6   23                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8   15                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11   15                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14    7   10                                                  
CONECT   16    2   17   21                                                  
CONECT   17   16   18                                                       
CONECT   18   17   19                                                       
CONECT   19   18   20                                                       
CONECT   20   19   21                                                       
CONECT   21   16   20   22                                                  
CONECT   22   21   23                                                       
CONECT   23   22    5   24                                                  
CONECT   24   23                                                            
MASTER        0    0    0    0    0    0    0    0   24    0   54    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₉H₁₇N₃O₂

Average Mass

319.3640 Da

Monoisotopic Mass

319.13208 Da

IUPAC Name

(3R)-3-[(1H-indol-3-yl)methyl]-4-methyl-2,3,4,5-tetrahydro-1H-1,4-benzodiazepine-2,5-dione

Traditional Name

(3R)-3-(1H-indol-3-ylmethyl)-4-methyl-1,3-dihydro-1,4-benzodiazepine-2,5-dione

CAS Registry Number

Not Available

SMILES

CN1[C@H](CC2=CNC3=CC=CC=C23)C(=O)NC2=C(C=CC=C2)C1=O

InChI Identifier

InChI=1S/C19H17N3O2/c1-22-17(10-12-11-20-15-8-4-2-6-13(12)15)18(23)21-16-9-5-3-7-14(16)19(22)24/h2-9,11,17,20H,10H2,1H3,(H,21,23)/t17-/m1/s1

InChI Key

QYBGEUDXQJVALS-QGZVFWFLSA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, Methanol-d4, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 150 MHz, Methanol-d4, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 250 MHz, Methanol-d4, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 175 MHz, Methanol-d4, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, Methanol-d4, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, Methanol-d4, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 225 MHz, Methanol-d4, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, Methanol-d4, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 125 MHz, Methanol-d4, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 25 MHz, Methanol-d4, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, Methanol-d4, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, Methanol-d4, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, Methanol-d4, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, Methanol-d4, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, Methanol-d4, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, Methanol-d4, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, Methanol-d4, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, Methanol-d4, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, Methanol-d4, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, Methanol-d4, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Malbranchea flavorosea

Chemical Taxonomy

Classification

Not classified

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	2.8	ALOGPS
logP	3.18	ChemAxon
logS	-3.6	ALOGPS
pKa (Strongest Acidic)	12.01	ChemAxon
pKa (Strongest Basic)	-1.8	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	2	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	65.2 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	93.43 m³·mol⁻¹	ChemAxon
Polarizability	32.15 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

Not Available

References

General References

Rebollar-Ramos D, Macias-Ruvalcaba ML, Figueroa M, Raja HA, Gonzalez-Andrade M, Mata R: Additional alpha-glucosidase inhibitors from Malbranchea flavorosea (Leotiomycetes, Ascomycota). J Antibiot (Tokyo). 2018 Oct;71(10):862-871. doi: 10.1038/s41429-018-0075-6. Epub 2018 Jul 17. [PubMed:30018423 ]

Showing NP-Card for (R)-3,4-dihydro-3-(1H-indol-3-ylmethyl)-4-methyl-1H-1,4-benzodiazepine-2,5-dione (NP0044126)

MOL for NP0044126 ((R)-3,4-dihydro-3-(1H-indol-3-ylmethyl)-4-methyl-1H-1,4-benzodiazepine-2,5-dione)

3D MOL for NP0044126 ((R)-3,4-dihydro-3-(1H-indol-3-ylmethyl)-4-methyl-1H-1,4-benzodiazepine-2,5-dione)

3D SDF for NP0044126 ((R)-3,4-dihydro-3-(1H-indol-3-ylmethyl)-4-methyl-1H-1,4-benzodiazepine-2,5-dione)

3D-SDF for NP0044126 ((R)-3,4-dihydro-3-(1H-indol-3-ylmethyl)-4-methyl-1H-1,4-benzodiazepine-2,5-dione)

PDB for NP0044126 ((R)-3,4-dihydro-3-(1H-indol-3-ylmethyl)-4-methyl-1H-1,4-benzodiazepine-2,5-dione)

3D PDB for NP0044126 ((R)-3,4-dihydro-3-(1H-indol-3-ylmethyl)-4-methyl-1H-1,4-benzodiazepine-2,5-dione)

SMILES for NP0044126 ((R)-3,4-dihydro-3-(1H-indol-3-ylmethyl)-4-methyl-1H-1,4-benzodiazepine-2,5-dione)

INCHI for NP0044126 ((R)-3,4-dihydro-3-(1H-indol-3-ylmethyl)-4-methyl-1H-1,4-benzodiazepine-2,5-dione)

Structure for NP0044126 ((R)-3,4-dihydro-3-(1H-indol-3-ylmethyl)-4-methyl-1H-1,4-benzodiazepine-2,5-dione)

3D Structure for NP0044126 ((R)-3,4-dihydro-3-(1H-indol-3-ylmethyl)-4-methyl-1H-1,4-benzodiazepine-2,5-dione)