NP-MRD: Showing NP-Card for 1-[3-(3-{[1-carboxy-3-(c-hydroxycarbonimidoyl)propyl]carbamoyl}-6-hydroxy-9h-pyrido[3,4-b]indol-1-yl)propanoyl]pyrrolidine-2-carboxylic acid (NP0318205)

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Record Information

Version

2.0

Created at

2022-09-11 18:33:55 UTC

Updated at

2022-09-11 18:33:55 UTC

NP-MRD ID

NP0318205

Secondary Accession Numbers

None

Natural Product Identification

Common Name

1-[3-(3-{[1-carboxy-3-(c-hydroxycarbonimidoyl)propyl]carbamoyl}-6-hydroxy-9h-pyrido[3,4-b]indol-1-yl)propanoyl]pyrrolidine-2-carboxylic acid

Description

1-[3-(3-{[1-Carboxy-3-(C-hydroxycarbonimidoyl)propyl]carbamoyl}-6-hydroxy-9H-pyrido[3,4-b]indol-1-yl)propanoyl]pyrrolidine-2-carboxylic acid belongs to the class of organic compounds known as harmala alkaloids. Harmala alkaloids are compounds with a structure based on harmaline, harmine, harmalol, harman or a derivative of those parents. These parents are beta-carbolines, consisting of a pyrimidine fused to the pyrrole moiety of an indole to form a pyrido[3,4-b]indole. 1-[3-(3-{[1-carboxy-3-(c-hydroxycarbonimidoyl)propyl]carbamoyl}-6-hydroxy-9h-pyrido[3,4-b]indol-1-yl)propanoyl]pyrrolidine-2-carboxylic acid is found in Mycena metata. Based on a literature review very few articles have been published on 1-[3-(3-{[1-carboxy-3-(C-hydroxycarbonimidoyl)propyl]carbamoyl}-6-hydroxy-9H-pyrido[3,4-b]indol-1-yl)propanoyl]pyrrolidine-2-carboxylic acid.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309112220332D          

 38 41  0  0  0  0            999 V2000
    5.0511    0.6328    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
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M  END

     RDKit          3D

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M  END


  Mrv1652309112220332D          

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 23 24  1  0  0  0  0
 24 25  1  0  0  0  0
 25 26  2  0  0  0  0
 25 27  1  0  0  0  0
 27 28  1  0  0  0  0
 28 29  1  0  0  0  0
 29 30  1  0  0  0  0
 30 31  1  0  0  0  0
 27 31  1  0  0  0  0
 31 32  1  0  0  0  0
 32 33  2  0  0  0  0
 32 34  1  0  0  0  0
 22 35  2  0  0  0  0
 10 35  1  0  0  0  0
  6 36  1  0  0  0  0
 36 37  2  0  0  0  0
 36 38  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0318205

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC(=N)CCC(NC(=O)C1=CC2=C(NC3=C2C=C(O)C=C3)C(CCC(=O)N2CCCC2C(O)=O)=N1)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C25H27N5O8/c26-20(32)7-5-17(24(35)36)29-23(34)18-11-14-13-10-12(31)3-4-15(13)28-22(14)16(27-18)6-8-21(33)30-9-1-2-19(30)25(37)38/h3-4,10-11,17,19,28,31H,1-2,5-9H2,(H2,26,32)(H,29,34)(H,35,36)(H,37,38)

> <INCHI_KEY>
NXSPJNGIASLZOG-UHFFFAOYSA-N

> <FORMULA>
C25H27N5O8

> <MOLECULAR_WEIGHT>
525.518

> <EXACT_MASS>
525.185962849

> <JCHEM_ACCEPTOR_COUNT>
10

> <JCHEM_ATOM_COUNT>
65

> <JCHEM_AVERAGE_POLARIZABILITY>
53.39747419129735

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
7

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
1-[3-(3-{[1-carboxy-3-(C-hydroxycarbonimidoyl)propyl]carbamoyl}-6-hydroxy-9H-pyrido[3,4-b]indol-1-yl)propanoyl]pyrrolidine-2-carboxylic acid

> <JCHEM_LOGP>
-2.2634066022722656

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
3.384841319729463

> <JCHEM_PKA_STRONGEST_ACIDIC>
-0.9063328250417211

> <JCHEM_PKA_STRONGEST_BASIC>
13.337032170317565

> <JCHEM_POLAR_SURFACE_AREA>
216.99999999999997

> <JCHEM_REFRACTIVITY>
141.4983

> <JCHEM_ROTATABLE_BOND_COUNT>
10

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
1-[3-(3-{[1-carboxy-3-(C-hydroxycarbonimidoyl)propyl]carbamoyl}-6-hydroxy-9H-pyrido[3,4-b]indol-1-yl)propanoyl]pyrrolidine-2-carboxylic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 11-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   11-SEP-22         0                                  
HETATM    1  N   UNK     0       9.429   1.181   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0      10.762   0.411   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0      10.762  -1.129   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0      12.096   1.181   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      13.430   0.411   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      14.763   1.181   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0      16.097   0.411   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0      17.431   1.181   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0      17.431   2.721   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0      18.764   0.411   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      18.764  -1.129   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      20.098  -1.899   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      21.432  -1.129   0.000  0.00  0.00           C+0
HETATM   14  N   UNK     0      22.576  -2.159   0.000  0.00  0.00           N+0
HETATM   15  C   UNK     0      21.950  -3.566   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      22.576  -4.973   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      21.671  -6.219   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      20.139  -6.058   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0      19.234  -7.304   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0      19.513  -4.651   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      20.418  -3.405   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      21.432   0.411   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      22.765   1.181   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      22.765   2.721   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      24.099   3.491   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0      25.433   2.721   0.000  0.00  0.00           O+0
HETATM   27  N   UNK     0      24.099   5.031   0.000  0.00  0.00           N+0
HETATM   28  C   UNK     0      22.853   5.936   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      23.329   7.401   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      24.869   7.401   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      25.345   5.936   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      26.810   5.461   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0      27.954   6.491   0.000  0.00  0.00           O+0
HETATM   34  O   UNK     0      27.130   3.954   0.000  0.00  0.00           O+0
HETATM   35  N   UNK     0      20.098   1.181   0.000  0.00  0.00           N+0
HETATM   36  C   UNK     0      14.763   2.721   0.000  0.00  0.00           C+0
HETATM   37  O   UNK     0      16.097   3.491   0.000  0.00  0.00           O+0
HETATM   38  O   UNK     0      13.430   3.491   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7   36                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8   11   35                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13   21                                                  
CONECT   13   12   14   22                                                  
CONECT   14   13   15                                                       
CONECT   15   14   16   21                                                  
CONECT   16   15   17                                                       
CONECT   17   16   18                                                       
CONECT   18   17   19   20                                                  
CONECT   19   18                                                            
CONECT   20   18   21                                                       
CONECT   21   20   15   12                                                  
CONECT   22   13   23   35                                                  
CONECT   23   22   24                                                       
CONECT   24   23   25                                                       
CONECT   25   24   26   27                                                  
CONECT   26   25                                                            
CONECT   27   25   28   31                                                  
CONECT   28   27   29                                                       
CONECT   29   28   30                                                       
CONECT   30   29   31                                                       
CONECT   31   30   27   32                                                  
CONECT   32   31   33   34                                                  
CONECT   33   32                                                            
CONECT   34   32                                                            
CONECT   35   22   10                                                       
CONECT   36    6   37   38                                                  
CONECT   37   36                                                            
CONECT   38   36                                                            
MASTER        0    0    0    0    0    0    0    0   38    0   82    0
END

View in JSmol

Synonyms

Value	Source
1-[3-(3-{[1-carboxy-3-(C-hydroxycarbonimidoyl)propyl]carbamoyl}-6-hydroxy-9H-pyrido[3,4-b]indol-1-yl)propanoyl]pyrrolidine-2-carboxylate	Generator

Chemical Formula

C₂₅H₂₇N₅O₈

Average Mass

525.5180 Da

Monoisotopic Mass

525.18596 Da

IUPAC Name

1-[3-(3-{[1-carboxy-3-(C-hydroxycarbonimidoyl)propyl]carbamoyl}-6-hydroxy-9H-pyrido[3,4-b]indol-1-yl)propanoyl]pyrrolidine-2-carboxylic acid

Traditional Name

1-[3-(3-{[1-carboxy-3-(C-hydroxycarbonimidoyl)propyl]carbamoyl}-6-hydroxy-9H-pyrido[3,4-b]indol-1-yl)propanoyl]pyrrolidine-2-carboxylic acid

CAS Registry Number

Not Available

SMILES

OC(=N)CCC(NC(=O)C1=CC2=C(NC3=C2C=C(O)C=C3)C(CCC(=O)N2CCCC2C(O)=O)=N1)C(O)=O

InChI Identifier

InChI=1S/C25H27N5O8/c26-20(32)7-5-17(24(35)36)29-23(34)18-11-14-13-10-12(31)3-4-15(13)28-22(14)16(27-18)6-8-21(33)30-9-1-2-19(30)25(37)38/h3-4,10-11,17,19,28,31H,1-2,5-9H2,(H2,26,32)(H,29,34)(H,35,36)(H,37,38)

InChI Key

NXSPJNGIASLZOG-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
Mycena metata	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as harmala alkaloids. Harmala alkaloids are compounds with a structure based on harmaline, harmine, harmalol, harman or a derivative of those parents. These parents are beta-carbolines, consisting of a pyrimidine fused to the pyrrole moiety of an indole to form a pyrido[3,4-b]indole.

Kingdom

Organic compounds

Super Class

Alkaloids and derivatives

Class

Harmala alkaloids

Sub Class

Not Available

Direct Parent

Harmala alkaloids

Alternative Parents

Substituents

Harman
Beta-carboline
N-acyl-alpha-amino acid
N-acyl-alpha amino acid or derivatives
Pyridoindole
Proline or derivatives
Hydroxyindole
Alpha-amino acid or derivatives
Indole or derivatives
Pyridine carboxylic acid or derivatives
Indole
N-acylpyrrolidine
2-heteroaryl carboxamide
Pyrrolidine carboxylic acid
Pyrrolidine carboxylic acid or derivatives
1-hydroxy-2-unsubstituted benzenoid
Dicarboxylic acid or derivatives
Benzenoid
Pyridine
Tertiary carboxylic acid amide
Heteroaromatic compound
Pyrrole
Pyrrolidine
Carboxamide group
Secondary carboxylic acid amide
Carboximidic acid
Carboximidic acid derivative
Carboxylic acid derivative
Carboxylic acid
Azacycle
Organoheterocyclic compound
Organopnictogen compound
Organic oxygen compound
Hydrocarbon derivative
Organic oxide
Organic nitrogen compound
Carbonyl group
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	-2.3	ChemAxon
pKa (Strongest Acidic)	-0.91	ChemAxon
pKa (Strongest Basic)	13.34	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	10	ChemAxon
Hydrogen Donor Count	7	ChemAxon
Polar Surface Area	217 Å²	ChemAxon
Rotatable Bond Count	10	ChemAxon
Refractivity	141.5 m³·mol⁻¹	ChemAxon
Polarizability	53.4 Å³	ChemAxon
Number of Rings	4	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	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

78119434

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for 1-[3-(3-{[1-carboxy-3-(c-hydroxycarbonimidoyl)propyl]carbamoyl}-6-hydroxy-9h-pyrido[3,4-b]indol-1-yl)propanoyl]pyrrolidine-2-carboxylic acid (NP0318205)

MOL for NP0318205 (1-[3-(3-{[1-carboxy-3-(c-hydroxycarbonimidoyl)propyl]carbamoyl}-6-hydroxy-9h-pyrido[3,4-b]indol-1-yl)propanoyl]pyrrolidine-2-carboxylic acid)

3D MOL for NP0318205 (1-[3-(3-{[1-carboxy-3-(c-hydroxycarbonimidoyl)propyl]carbamoyl}-6-hydroxy-9h-pyrido[3,4-b]indol-1-yl)propanoyl]pyrrolidine-2-carboxylic acid)

3D SDF for NP0318205 (1-[3-(3-{[1-carboxy-3-(c-hydroxycarbonimidoyl)propyl]carbamoyl}-6-hydroxy-9h-pyrido[3,4-b]indol-1-yl)propanoyl]pyrrolidine-2-carboxylic acid)

3D-SDF for NP0318205 (1-[3-(3-{[1-carboxy-3-(c-hydroxycarbonimidoyl)propyl]carbamoyl}-6-hydroxy-9h-pyrido[3,4-b]indol-1-yl)propanoyl]pyrrolidine-2-carboxylic acid)

PDB for NP0318205 (1-[3-(3-{[1-carboxy-3-(c-hydroxycarbonimidoyl)propyl]carbamoyl}-6-hydroxy-9h-pyrido[3,4-b]indol-1-yl)propanoyl]pyrrolidine-2-carboxylic acid)

3D PDB for NP0318205 (1-[3-(3-{[1-carboxy-3-(c-hydroxycarbonimidoyl)propyl]carbamoyl}-6-hydroxy-9h-pyrido[3,4-b]indol-1-yl)propanoyl]pyrrolidine-2-carboxylic acid)

SMILES for NP0318205 (1-[3-(3-{[1-carboxy-3-(c-hydroxycarbonimidoyl)propyl]carbamoyl}-6-hydroxy-9h-pyrido[3,4-b]indol-1-yl)propanoyl]pyrrolidine-2-carboxylic acid)

INCHI for NP0318205 (1-[3-(3-{[1-carboxy-3-(c-hydroxycarbonimidoyl)propyl]carbamoyl}-6-hydroxy-9h-pyrido[3,4-b]indol-1-yl)propanoyl]pyrrolidine-2-carboxylic acid)

Structure for NP0318205 (1-[3-(3-{[1-carboxy-3-(c-hydroxycarbonimidoyl)propyl]carbamoyl}-6-hydroxy-9h-pyrido[3,4-b]indol-1-yl)propanoyl]pyrrolidine-2-carboxylic acid)

3D Structure for NP0318205 (1-[3-(3-{[1-carboxy-3-(c-hydroxycarbonimidoyl)propyl]carbamoyl}-6-hydroxy-9h-pyrido[3,4-b]indol-1-yl)propanoyl]pyrrolidine-2-carboxylic acid)