NP-MRD: Showing NP-Card for 3-(1h-indol-3-ylmethyl)-6-(sec-butyl)-3,6-dihydropyrazine-2,5-diol (NP0207292)

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Record Information

Version

2.0

Created at

2022-09-05 03:50:45 UTC

Updated at

2022-09-05 03:50:45 UTC

NP-MRD ID

NP0207292

Secondary Accession Numbers

None

Natural Product Identification

Common Name

3-(1h-indol-3-ylmethyl)-6-(sec-butyl)-3,6-dihydropyrazine-2,5-diol

Description

3-(Butan-2-yl)-6-[(1H-indol-3-yl)methyl]-3,6-dihydropyrazine-2,5-diol 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. 3-(1h-indol-3-ylmethyl)-6-(sec-butyl)-3,6-dihydropyrazine-2,5-diol is found in Penicillium brevicompactum. 3-(Butan-2-yl)-6-[(1H-indol-3-yl)methyl]-3,6-dihydropyrazine-2,5-diol is an extremely weak basic (essentially neutral) compound (based on its pKa).

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 43 45  0  0  0  0  0  0  0  0999 V2000
   -5.2675   -1.4116   -0.6953 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0618   -0.6288   -1.1850 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5038    0.2548   -0.0910 C   0  0  2  0  0  0  0  0  0  0  0  0
   -4.5176    1.2508    0.4026 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2471    0.9032   -0.6029 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.3017   -0.1303   -0.9441 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1529   -0.3879   -0.1143 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1972   -1.6041    0.0771 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5360    0.7709    0.4530 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.4679    0.4390    1.5892 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5284   -0.4995    1.1452 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6193   -1.8423    1.4215 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7315   -2.2911    0.8281 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.3509   -1.2854    0.1855 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5282   -1.2712   -0.5640 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9093   -0.0649   -1.1051 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1798    1.0822   -0.9280 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0207    1.0601   -0.1880 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6233   -0.1534    0.3652 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4323    1.7475    0.9100 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6985    1.9163    0.2930 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3438    2.9558    0.5303 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3657   -2.2994   -1.3653 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2023   -0.8332   -0.7918 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0907   -1.8033    0.3187 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3398   -0.0944   -2.0920 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2892   -1.4226   -1.3984 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2474   -0.4109    0.7588 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6446    2.1184   -0.2425 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4920    0.7506    0.5181 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1962    1.5484    1.4404 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5145    1.4116   -1.5744 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4612   -0.6923   -1.8048 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1548    1.2104   -0.3804 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9426    1.3628    1.9792 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8841   -0.0677    2.3873 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9251   -2.4567    2.0173 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1040   -3.2778    0.8373 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.1121   -2.1810   -0.7081 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.8242    0.0140   -1.7045 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4742    2.0442   -1.3536 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4113    1.9323   -0.0179 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1547    2.3364    1.7291 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
  3  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  2  0
  7  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  2  0
 12 13  1  0
 13 14  1  0
 14 15  2  0
 15 16  1  0
 16 17  2  0
 17 18  1  0
 18 19  2  0
  9 20  1  0
 20 21  1  0
 21 22  2  0
 21  5  1  0
 19 11  1  0
 19 14  1  0
  1 23  1  0
  1 24  1  0
  1 25  1  0
  2 26  1  0
  2 27  1  0
  3 28  1  1
  4 29  1  0
  4 30  1  0
  4 31  1  0
  5 32  1  6
  6 33  1  0
  9 34  1  6
 10 35  1  0
 10 36  1  0
 12 37  1  0
 13 38  1  0
 15 39  1  0
 16 40  1  0
 17 41  1  0
 18 42  1  0
 20 43  1  0
M  END


  Mrv1533004171520562D          

 22 24  0  0  0  0            999 V2000
   -3.4060   -3.7923    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5990   -3.6207    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3441   -2.8361    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8961   -2.2230    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5371   -2.6646    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2822   -1.8800    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4752   -1.7084    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2203   -0.9238    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0768   -2.3215    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8838   -2.1500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387   -1.3654    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6538   -0.6979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387   -0.0305    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233   -0.2854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    0.1271    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523   -0.2854    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
    2.6378   -1.5229    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
   -0.1781   -3.1062    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9851   -3.2777    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2400   -4.0623    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
  3  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  7  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  2  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  2  0  0  0  0
 15 16  1  0  0  0  0
 16 17  2  0  0  0  0
 17 18  1  0  0  0  0
 18 19  2  0  0  0  0
 11 19  1  0  0  0  0
 14 19  1  0  0  0  0
  9 20  1  0  0  0  0
 20 21  1  0  0  0  0
  5 21  1  0  0  0  0
 21 22  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0207292

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CCC(C)C1NC(=O)C(CC2=CNC3=CC=CC=C23)NC1=O

> <INCHI_IDENTIFIER>
InChI=1S/C17H21N3O2/c1-3-10(2)15-17(22)19-14(16(21)20-15)8-11-9-18-13-7-5-4-6-12(11)13/h4-7,9-10,14-15,18H,3,8H2,1-2H3,(H,19,22)(H,20,21)

> <INCHI_KEY>
PGCNHGBQEYFZEX-UHFFFAOYSA-N

> <FORMULA>
C17H21N3O2

> <MOLECULAR_WEIGHT>
299.374

> <EXACT_MASS>
299.163376928

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
43

> <JCHEM_AVERAGE_POLARIZABILITY>
31.214429964838573

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
3-(butan-2-yl)-6-[(1H-indol-3-yl)methyl]piperazine-2,5-dione

> <ALOGPS_LOGP>
2.02

> <JCHEM_LOGP>
2.014114252333332

> <ALOGPS_LOGS>
-3.34

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.308800050089992

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.228294091542487

> <JCHEM_PKA_STRONGEST_BASIC>
-3.7610856097863246

> <JCHEM_POLAR_SURFACE_AREA>
73.99000000000001

> <JCHEM_REFRACTIVITY>
83.8969

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.38e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-(1H-indol-3-ylmethyl)-6-(sec-butyl)piperazine-2,5-dione

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 17-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   17-APR-15         0                                  
HETATM    1  C   UNK     0      -6.358  -7.079   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -4.852  -6.759   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -4.376  -5.294   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -5.406  -4.150   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -2.869  -4.974   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0      -2.393  -3.509   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0      -0.887  -3.189   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      -0.411  -1.724   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       0.143  -4.334   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       1.650  -4.013   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       2.126  -2.549   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       1.220  -1.303   0.000  0.00  0.00           C+0
HETATM   13  N   UNK     0       2.126  -0.057   0.000  0.00  0.00           N+0
HETATM   14  C   UNK     0       3.590  -0.533   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       4.924   0.237   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       6.258  -0.533   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       6.258  -2.073   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       4.924  -2.843   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       3.590  -2.073   0.000  0.00  0.00           C+0
HETATM   20  N   UNK     0      -0.333  -5.798   0.000  0.00  0.00           N+0
HETATM   21  C   UNK     0      -1.839  -6.118   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0      -2.315  -7.583   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6   21                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10   20                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12   19                                                  
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15   19                                                  
CONECT   15   14   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16   18                                                       
CONECT   18   17   19                                                       
CONECT   19   18   11   14                                                  
CONECT   20    9   21                                                       
CONECT   21   20    5   22                                                  
CONECT   22   21                                                            
MASTER        0    0    0    0    0    0    0    0   22    0   48    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₇H₂₁N₃O₂

Average Mass

299.3740 Da

Monoisotopic Mass

299.16338 Da

IUPAC Name

3-(butan-2-yl)-6-[(1H-indol-3-yl)methyl]piperazine-2,5-dione

Traditional Name

3-(1H-indol-3-ylmethyl)-6-(sec-butyl)piperazine-2,5-dione

CAS Registry Number

Not Available

SMILES

CCC(C)C1NC(=O)C(CC2=CNC3=CC=CC=C23)NC1=O

InChI Identifier

InChI=1S/C17H21N3O2/c1-3-10(2)15-17(22)19-14(16(21)20-15)8-11-9-18-13-7-5-4-6-12(11)13/h4-7,9-10,14-15,18H,3,8H2,1-2H3,(H,19,22)(H,20,21)

InChI Key

PGCNHGBQEYFZEX-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

Species Name	Source	Reference
Penicillium brevicompactum	LOTUS Database	35616633

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.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Indoles and derivatives

Sub Class

Indoles

Direct Parent

3-alkylindoles

Alternative Parents

Substituents

3-alkylindole
Benzenoid
Substituted pyrrole
Heteroaromatic compound
Cyclic carboximidic acid
Pyrrole
Azacycle
Organic 1,3-dipolar compound
Propargyl-type 1,3-dipolar organic compound
Organic nitrogen compound
Organic oxygen compound
Hydrocarbon derivative
Organooxygen compound
Organonitrogen 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	2.02	ALOGPS
logP	2.01	ChemAxon
logS	-3.3	ALOGPS
pKa (Strongest Acidic)	11.23	ChemAxon
pKa (Strongest Basic)	-3.8	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	2	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	73.99 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	83.9 m³·mol⁻¹	ChemAxon
Polarizability	31.21 Å³	ChemAxon
Number of Rings	3	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

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References

General References

LOTUS database [Link]

Showing NP-Card for 3-(1h-indol-3-ylmethyl)-6-(sec-butyl)-3,6-dihydropyrazine-2,5-diol (NP0207292)

MOL for NP0207292 (3-(1h-indol-3-ylmethyl)-6-(sec-butyl)-3,6-dihydropyrazine-2,5-diol)

3D MOL for NP0207292 (3-(1h-indol-3-ylmethyl)-6-(sec-butyl)-3,6-dihydropyrazine-2,5-diol)

3D SDF for NP0207292 (3-(1h-indol-3-ylmethyl)-6-(sec-butyl)-3,6-dihydropyrazine-2,5-diol)

3D-SDF for NP0207292 (3-(1h-indol-3-ylmethyl)-6-(sec-butyl)-3,6-dihydropyrazine-2,5-diol)

PDB for NP0207292 (3-(1h-indol-3-ylmethyl)-6-(sec-butyl)-3,6-dihydropyrazine-2,5-diol)

3D PDB for NP0207292 (3-(1h-indol-3-ylmethyl)-6-(sec-butyl)-3,6-dihydropyrazine-2,5-diol)

SMILES for NP0207292 (3-(1h-indol-3-ylmethyl)-6-(sec-butyl)-3,6-dihydropyrazine-2,5-diol)

INCHI for NP0207292 (3-(1h-indol-3-ylmethyl)-6-(sec-butyl)-3,6-dihydropyrazine-2,5-diol)

Structure for NP0207292 (3-(1h-indol-3-ylmethyl)-6-(sec-butyl)-3,6-dihydropyrazine-2,5-diol)

3D Structure for NP0207292 (3-(1h-indol-3-ylmethyl)-6-(sec-butyl)-3,6-dihydropyrazine-2,5-diol)