NP-MRD: Showing NP-Card for methyl 5-(hydroxymethyl)-6-methyl-4-{9h-pyrido[3,4-b]indol-1-ylmethyl}-5,6-dihydro-4h-pyran-3-carboxylate (NP0219526)

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Record Information

Version

2.0

Created at

2022-09-05 20:32:27 UTC

Updated at

2022-09-05 20:32:27 UTC

NP-MRD ID

NP0219526

Secondary Accession Numbers

None

Natural Product Identification

Common Name

methyl 5-(hydroxymethyl)-6-methyl-4-{9h-pyrido[3,4-b]indol-1-ylmethyl}-5,6-dihydro-4h-pyran-3-carboxylate

Description

Methyl 3-(hydroxymethyl)-2-methyl-4-({9H-pyrido[3,4-b]indol-1-yl}methyl)-3,4-dihydro-2H-pyran-5-carboxylate 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. Based on a literature review very few articles have been published on methyl 3-(hydroxymethyl)-2-methyl-4-({9H-pyrido[3,4-b]indol-1-yl}methyl)-3,4-dihydro-2H-pyran-5-carboxylate.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652309052222322D          

 27 30  0  0  0  0            999 V2000
    3.8761   -4.1237    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4281   -3.5106    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1732   -2.7260    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3662   -2.5545    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.7252   -2.1129    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5322   -2.2844    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0842   -1.6713    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.8293   -0.8867    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.3813   -0.2736    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0223   -0.7152    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7674    0.0694    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3194    0.6825    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.4703   -1.3283    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6633   -1.1567    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4084   -0.3721    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9604    0.2410    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.7054    1.0256    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8985    1.1971    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3464    0.5840    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6014   -0.2006    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9339   -0.6855    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.2665   -0.2006    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4595   -0.3721    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0925    0.2410    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1624    1.0256    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9694    1.1971    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5214    0.5840    0.0000 C   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  2  0  0  0  0
  3  5  1  0  0  0  0
  5  6  2  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
  8 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 10 13  1  0  0  0  0
  5 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  2  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
 15 20  1  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
 23 24  2  0  0  0  0
 24 25  1  0  0  0  0
 25 26  2  0  0  0  0
 26 27  1  0  0  0  0
 22 27  2  0  0  0  0
 19 27  1  0  0  0  0
M  END


  Mrv1652309052222322D          

 27 30  0  0  0  0            999 V2000
    3.8761   -4.1237    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4281   -3.5106    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1732   -2.7260    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3662   -2.5545    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.7252   -2.1129    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5322   -2.2844    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0842   -1.6713    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.8293   -0.8867    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.3813   -0.2736    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0223   -0.7152    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7674    0.0694    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3194    0.6825    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.4703   -1.3283    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6633   -1.1567    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4084   -0.3721    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9604    0.2410    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.7054    1.0256    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8985    1.1971    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3464    0.5840    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6014   -0.2006    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9339   -0.6855    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.2665   -0.2006    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4595   -0.3721    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0925    0.2410    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1624    1.0256    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9694    1.1971    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5214    0.5840    0.0000 C   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  2  0  0  0  0
  3  5  1  0  0  0  0
  5  6  2  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
  8 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 10 13  1  0  0  0  0
  5 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  2  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
 15 20  1  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
 23 24  2  0  0  0  0
 24 25  1  0  0  0  0
 25 26  2  0  0  0  0
 26 27  1  0  0  0  0
 22 27  2  0  0  0  0
 19 27  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0219526

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC(=O)C1=COC(C)C(CO)C1CC1=NC=CC2=C1NC1=C2C=CC=C1

> <INCHI_IDENTIFIER>
InChI=1S/C21H22N2O4/c1-12-16(10-24)15(17(11-27-12)21(25)26-2)9-19-20-14(7-8-22-19)13-5-3-4-6-18(13)23-20/h3-8,11-12,15-16,23-24H,9-10H2,1-2H3

> <INCHI_KEY>
HNPBJGUAULGPHG-UHFFFAOYSA-N

> <FORMULA>
C21H22N2O4

> <MOLECULAR_WEIGHT>
366.417

> <EXACT_MASS>
366.157957196

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
49

> <JCHEM_AVERAGE_POLARIZABILITY>
38.9816072776151

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
methyl 3-(hydroxymethyl)-2-methyl-4-({9H-pyrido[3,4-b]indol-1-yl}methyl)-3,4-dihydro-2H-pyran-5-carboxylate

> <JCHEM_LOGP>
1.8268769749999998

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
15.375790390588826

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.598057239199253

> <JCHEM_PKA_STRONGEST_BASIC>
5.665848280577124

> <JCHEM_POLAR_SURFACE_AREA>
84.44

> <JCHEM_REFRACTIVITY>
100.81430000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
methyl 5-(hydroxymethyl)-6-methyl-4-{9H-pyrido[3,4-b]indol-1-ylmethyl}-5,6-dihydro-4H-pyran-3-carboxylate

> <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       7.235  -7.698   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0       8.266  -6.553   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0       7.790  -5.089   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       6.284  -4.768   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       8.820  -3.944   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      10.327  -4.264   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      11.357  -3.120   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0      10.881  -1.655   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      11.912  -0.511   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       9.375  -1.335   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       8.899   0.130   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       9.930   1.274   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0       8.344  -2.479   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       6.838  -2.159   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       6.362  -0.695   0.000  0.00  0.00           C+0
HETATM   16  N   UNK     0       7.393   0.450   0.000  0.00  0.00           N+0
HETATM   17  C   UNK     0       6.917   1.914   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       5.410   2.235   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       4.380   1.090   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       4.856  -0.374   0.000  0.00  0.00           C+0
HETATM   21  N   UNK     0       3.610  -1.280   0.000  0.00  0.00           N+0
HETATM   22  C   UNK     0       2.364  -0.374   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       0.858  -0.695   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      -0.173   0.450   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       0.303   1.914   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       1.810   2.235   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       2.840   1.090   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6   13                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8   11   13                                                  
CONECT   11   10   12                                                       
CONECT   12   11                                                            
CONECT   13   10    5   14                                                  
CONECT   14   13   15                                                       
CONECT   15   14   16   20                                                  
CONECT   16   15   17                                                       
CONECT   17   16   18                                                       
CONECT   18   17   19                                                       
CONECT   19   18   20   27                                                  
CONECT   20   19   15   21                                                  
CONECT   21   20   22                                                       
CONECT   22   21   23   27                                                  
CONECT   23   22   24                                                       
CONECT   24   23   25                                                       
CONECT   25   24   26                                                       
CONECT   26   25   27                                                       
CONECT   27   26   22   19                                                  
MASTER        0    0    0    0    0    0    0    0   27    0   60    0
END

View in JSmol

Synonyms

Value	Source
Methyl 3-(hydroxymethyl)-2-methyl-4-({9h-pyrido[3,4-b]indol-1-yl}methyl)-3,4-dihydro-2H-pyran-5-carboxylic acid	Generator

Chemical Formula

C₂₁H₂₂N₂O₄

Average Mass

366.4170 Da

Monoisotopic Mass

366.15796 Da

IUPAC Name

methyl 3-(hydroxymethyl)-2-methyl-4-({9H-pyrido[3,4-b]indol-1-yl}methyl)-3,4-dihydro-2H-pyran-5-carboxylate

Traditional Name

methyl 5-(hydroxymethyl)-6-methyl-4-{9H-pyrido[3,4-b]indol-1-ylmethyl}-5,6-dihydro-4H-pyran-3-carboxylate

CAS Registry Number

Not Available

SMILES

COC(=O)C1=COC(C)C(CO)C1CC1=NC=CC2=C1NC1=C2C=CC=C1

InChI Identifier

InChI=1S/C21H22N2O4/c1-12-16(10-24)15(17(11-27-12)21(25)26-2)9-19-20-14(7-8-22-19)13-5-3-4-6-18(13)23-20/h3-8,11-12,15-16,23-24H,9-10H2,1-2H3

InChI Key

HNPBJGUAULGPHG-UHFFFAOYSA-N

Experimental Spectra

Not Available

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Not Available

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
Pyridoindole
Indole
Indole or derivatives
Pyridine
Benzenoid
Heteroaromatic compound
Pyrrole
Methyl ester
Enoate ester
Alpha,beta-unsaturated carboxylic ester
Vinylogous ester
Carboxylic acid ester
Azacycle
Organoheterocyclic compound
Oxacycle
Carboxylic acid derivative
Monocarboxylic acid or derivatives
Organic nitrogen compound
Organonitrogen compound
Organooxygen compound
Organic oxide
Organopnictogen compound
Organic oxygen compound
Carbonyl group
Primary alcohol
Hydrocarbon derivative
Alcohol
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	1.83	ChemAxon
pKa (Strongest Acidic)	13.6	ChemAxon
pKa (Strongest Basic)	5.67	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	84.44 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	100.81 m³·mol⁻¹	ChemAxon
Polarizability	38.98 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

162901548

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for methyl 5-(hydroxymethyl)-6-methyl-4-{9h-pyrido[3,4-b]indol-1-ylmethyl}-5,6-dihydro-4h-pyran-3-carboxylate (NP0219526)

MOL for NP0219526 (methyl 5-(hydroxymethyl)-6-methyl-4-{9h-pyrido[3,4-b]indol-1-ylmethyl}-5,6-dihydro-4h-pyran-3-carboxylate)

3D MOL for NP0219526 (methyl 5-(hydroxymethyl)-6-methyl-4-{9h-pyrido[3,4-b]indol-1-ylmethyl}-5,6-dihydro-4h-pyran-3-carboxylate)

3D SDF for NP0219526 (methyl 5-(hydroxymethyl)-6-methyl-4-{9h-pyrido[3,4-b]indol-1-ylmethyl}-5,6-dihydro-4h-pyran-3-carboxylate)

3D-SDF for NP0219526 (methyl 5-(hydroxymethyl)-6-methyl-4-{9h-pyrido[3,4-b]indol-1-ylmethyl}-5,6-dihydro-4h-pyran-3-carboxylate)

PDB for NP0219526 (methyl 5-(hydroxymethyl)-6-methyl-4-{9h-pyrido[3,4-b]indol-1-ylmethyl}-5,6-dihydro-4h-pyran-3-carboxylate)

3D PDB for NP0219526 (methyl 5-(hydroxymethyl)-6-methyl-4-{9h-pyrido[3,4-b]indol-1-ylmethyl}-5,6-dihydro-4h-pyran-3-carboxylate)

SMILES for NP0219526 (methyl 5-(hydroxymethyl)-6-methyl-4-{9h-pyrido[3,4-b]indol-1-ylmethyl}-5,6-dihydro-4h-pyran-3-carboxylate)

INCHI for NP0219526 (methyl 5-(hydroxymethyl)-6-methyl-4-{9h-pyrido[3,4-b]indol-1-ylmethyl}-5,6-dihydro-4h-pyran-3-carboxylate)

Structure for NP0219526 (methyl 5-(hydroxymethyl)-6-methyl-4-{9h-pyrido[3,4-b]indol-1-ylmethyl}-5,6-dihydro-4h-pyran-3-carboxylate)

3D Structure for NP0219526 (methyl 5-(hydroxymethyl)-6-methyl-4-{9h-pyrido[3,4-b]indol-1-ylmethyl}-5,6-dihydro-4h-pyran-3-carboxylate)