NP-MRD: Showing NP-Card for methyl (4as,7as)-1-hydroxy-7-(hydroxymethyl)-4ah,5h,7ah-cyclopenta[c]pyridine-4-carboxylate (NP0229262)

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Record Information

Version

2.0

Created at

2022-09-06 09:14:23 UTC

Updated at

2022-09-06 09:14:23 UTC

NP-MRD ID

NP0229262

Secondary Accession Numbers

None

Natural Product Identification

Common Name

methyl (4as,7as)-1-hydroxy-7-(hydroxymethyl)-4ah,5h,7ah-cyclopenta[c]pyridine-4-carboxylate

Description

Gardenamide belongs to the class of organic compounds known as tetrahydropyridines. These are derivatives of pyridine in which two double bonds in the pyridine moiety are reduced by adding four hydrogen atoms. methyl (4as,7as)-1-hydroxy-7-(hydroxymethyl)-4ah,5h,7ah-cyclopenta[c]pyridine-4-carboxylate is found in Gardenia jasminoides and Rothmannia urcelliformis. methyl (4as,7as)-1-hydroxy-7-(hydroxymethyl)-4ah,5h,7ah-cyclopenta[c]pyridine-4-carboxylate was first documented in 2007 (PMID: 17365698). Based on a literature review a small amount of articles have been published on Gardenamide (PMID: 31391892) (PMID: 26402670) (PMID: 26389892) (PMID: 25485482).

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 29 30  0  0  0  0  0  0  0  0999 V2000
    4.9489    0.3803   -0.0057 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7058   -0.0788   -0.5256 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5454   -0.0005    0.2312 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6492    0.4901    1.3827 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2413   -0.4748   -0.2964 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1663   -0.9821   -1.5027 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0812   -1.4236   -1.9757 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1685   -1.3765   -1.3271 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3739   -1.8539   -1.9104 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2048   -0.8272    0.0435 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.1576    0.3469    0.1039 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5883    0.3026   -0.3296 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1806    1.5406   -0.1447 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5452    1.4053    0.5909 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1451    1.1075    0.9161 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0581   -0.3419    0.5882 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.7879    1.3460    0.5020 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2706   -0.3628    0.7790 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.6725    0.4333   -0.8338 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0782   -1.0414   -2.0933 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7183   -2.7690   -1.6756 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6587   -1.6555    0.7005 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0924   -0.4133    0.3521 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6859    0.0138   -1.3960 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3441    1.6721    0.8129 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0544    2.3772    0.7232 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1186    1.3379    1.9689 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5019    1.7640    0.2959 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2543   -0.9163    1.5556 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  3  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  2  0
  8  9  1  0
  8 10  1  0
 10 16  1  0
 16 15  1  0
 15 14  1  0
 14 11  2  0
 11 12  1  0
 12 13  1  0
 16  5  1  0
 11 10  1  0
  1 17  1  0
  1 18  1  0
  1 19  1  0
  6 20  1  0
  9 21  1  0
 10 22  1  1
 16 29  1  1
 15 27  1  0
 15 28  1  0
 14 26  1  0
 12 23  1  0
 12 24  1  0
 13 25  1  0
M  END


  Mrv1652309062211142D          

 16 17  0  0  1  0            999 V2000
    3.9934    3.3000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9934    2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2789    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5645    2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2789    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9934    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9934    0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.2789   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2789   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5645    0.0000    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.7798   -0.2549    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5249   -1.0396    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0769   -1.6527    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2949    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7798    1.0799    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5645    0.8250    0.0000 C   0  0  2  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  2  0  0  0  0
  8  9  1  0  0  0  0
  8 10  1  0  0  0  0
 10 11  1  6  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 11 14  2  0  0  0  0
 14 15  1  0  0  0  0
 16 15  1  6  0  0  0
  5 16  1  0  0  0  0
 10 16  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0229262

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC(=O)C1=CN=C(O)[C@H]2[C@@H]1CC=C2CO

> <INCHI_IDENTIFIER>
InChI=1S/C11H13NO4/c1-16-11(15)8-4-12-10(14)9-6(5-13)2-3-7(8)9/h2,4,7,9,13H,3,5H2,1H3,(H,12,14)/t7-,9-/m1/s1

> <INCHI_KEY>
JKUVCURZAWEADG-VXNVDRBHSA-N

> <FORMULA>
C11H13NO4

> <MOLECULAR_WEIGHT>
223.228

> <EXACT_MASS>
223.084457903

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
29

> <JCHEM_AVERAGE_POLARIZABILITY>
21.99756241115553

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
methyl (4aS,7aS)-1-hydroxy-7-(hydroxymethyl)-4aH,5H,7aH-cyclopenta[c]pyridine-4-carboxylate

> <JCHEM_LOGP>
-0.07765960599999963

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
15.1533483283829

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.89410818383608

> <JCHEM_PKA_STRONGEST_BASIC>
2.846388447266477

> <JCHEM_POLAR_SURFACE_AREA>
79.12

> <JCHEM_REFRACTIVITY>
57.3372

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
methyl (4aS,7aS)-1-hydroxy-7-(hydroxymethyl)-4aH,5H,7aH-cyclopenta[c]pyridine-4-carboxylate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 06-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-SEP-22         0                                  
HETATM    1  C   UNK     0       7.454   6.160   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0       7.454   4.620   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0       6.121   3.850   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       4.787   4.620   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       6.121   2.310   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       7.454   1.540   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0       7.454   0.000   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0       6.121  -0.770   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       6.121  -2.310   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0       4.787   0.000   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       3.322  -0.476   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       2.846  -1.941   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       3.877  -3.085   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0       2.417   0.770   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       3.322   2.016   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       4.787   1.540   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   16                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8   11   16                                                  
CONECT   11   10   12   14                                                  
CONECT   12   11   13                                                       
CONECT   13   12                                                            
CONECT   14   11   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15    5   10                                                  
MASTER        0    0    0    0    0    0    0    0   16    0   34    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₁H₁₃NO₄

Average Mass

223.2280 Da

Monoisotopic Mass

223.08446 Da

IUPAC Name

methyl (4aS,7aS)-1-hydroxy-7-(hydroxymethyl)-4aH,5H,7aH-cyclopenta[c]pyridine-4-carboxylate

Traditional Name

methyl (4aS,7aS)-1-hydroxy-7-(hydroxymethyl)-4aH,5H,7aH-cyclopenta[c]pyridine-4-carboxylate

CAS Registry Number

Not Available

SMILES

COC(=O)C1=CN=C(O)[C@H]2[C@@H]1CC=C2CO

InChI Identifier

InChI=1S/C11H13NO4/c1-16-11(15)8-4-12-10(14)9-6(5-13)2-3-7(8)9/h2,4,7,9,13H,3,5H2,1H3,(H,12,14)/t7-,9-/m1/s1

InChI Key

JKUVCURZAWEADG-VXNVDRBHSA-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
Gardenia jasminoides	LOTUS Database	35616633
Rothmannia urcelliformis	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as tetrahydropyridines. These are derivatives of pyridine in which two double bonds in the pyridine moiety are reduced by adding four hydrogen atoms.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Pyridines and derivatives

Sub Class

Hydropyridines

Direct Parent

Tetrahydropyridines

Alternative Parents

Substituents

Tetrahydropyridine
Methyl ester
Enoate ester
Alpha,beta-unsaturated carboxylic ester
Vinylogous amide
Carboxamide group
Carboxylic acid ester
Lactam
Secondary carboxylic acid amide
Monocarboxylic acid or derivatives
Carboxylic acid derivative
Azacycle
Organic nitrogen compound
Alcohol
Primary alcohol
Organooxygen compound
Organonitrogen compound
Carbonyl group
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic 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	-0.078	ChemAxon
pKa (Strongest Acidic)	4.89	ChemAxon
pKa (Strongest Basic)	2.85	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	79.12 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	57.34 m³·mol⁻¹	ChemAxon
Polarizability	22 Å³	ChemAxon
Number of Rings	2	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

C00032629

Chemspider ID

8950755

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

10775442

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Zhang Z, Wang Y, Zhang Y, Li J, Huang W, Wang L: The synthesis and biological evaluation of novel gardenamide A derivatives as multifunctional neuroprotective agents. Medchemcomm. 2019 May 24;10(7):1180-1186. doi: 10.1039/c9md00211a. eCollection 2019 Jul 1. [PubMed:31391892 ]
Zhao J, Peng L, Zheng W, Wang R, Zhang L, Yang J, Chen H: Chemically Bonding of Amantadine with Gardenamide A Enhances the Neuroprotective Effects against Corticosterone-Induced Insults in PC12 Cells. Int J Mol Sci. 2015 Sep 21;16(9):22795-810. doi: 10.3390/ijms160922795. [PubMed:26402670 ]
Wang R, Peng L, Zhao J, Zhang L, Guo C, Zheng W, Chen H: Gardenamide A Protects RGC-5 Cells from H(2)O(2)-Induced Oxidative Stress Insults by Activating PI3K/Akt/eNOS Signaling Pathway. Int J Mol Sci. 2015 Sep 15;16(9):22350-67. doi: 10.3390/ijms160922350. [PubMed:26389892 ]
Wang R, Yang J, Peng L, Zhao J, Mu N, Huang J, Lazarovici P, Chen H, Zheng W: Gardenamide A attenuated cell apoptosis induced by serum deprivation insult via the ERK1/2 and PI3K/AKT signaling pathways. Neuroscience. 2015 Feb 12;286:242-50. doi: 10.1016/j.neuroscience.2014.11.056. Epub 2014 Dec 6. [PubMed:25485482 ]
Juma BF, Majinda RR: Constituents of Gardenia volkensii: their brine shrimp lethality and DPPH radical scavenging properties. Nat Prod Res. 2007 Feb;21(2):121-5. doi: 10.1080/14786410600905907. [PubMed:17365698 ]
LOTUS database [Link]

Showing NP-Card for methyl (4as,7as)-1-hydroxy-7-(hydroxymethyl)-4ah,5h,7ah-cyclopenta[c]pyridine-4-carboxylate (NP0229262)

MOL for NP0229262 (methyl (4as,7as)-1-hydroxy-7-(hydroxymethyl)-4ah,5h,7ah-cyclopenta[c]pyridine-4-carboxylate)

3D MOL for NP0229262 (methyl (4as,7as)-1-hydroxy-7-(hydroxymethyl)-4ah,5h,7ah-cyclopenta[c]pyridine-4-carboxylate)

3D SDF for NP0229262 (methyl (4as,7as)-1-hydroxy-7-(hydroxymethyl)-4ah,5h,7ah-cyclopenta[c]pyridine-4-carboxylate)

3D-SDF for NP0229262 (methyl (4as,7as)-1-hydroxy-7-(hydroxymethyl)-4ah,5h,7ah-cyclopenta[c]pyridine-4-carboxylate)

PDB for NP0229262 (methyl (4as,7as)-1-hydroxy-7-(hydroxymethyl)-4ah,5h,7ah-cyclopenta[c]pyridine-4-carboxylate)

3D PDB for NP0229262 (methyl (4as,7as)-1-hydroxy-7-(hydroxymethyl)-4ah,5h,7ah-cyclopenta[c]pyridine-4-carboxylate)

SMILES for NP0229262 (methyl (4as,7as)-1-hydroxy-7-(hydroxymethyl)-4ah,5h,7ah-cyclopenta[c]pyridine-4-carboxylate)

INCHI for NP0229262 (methyl (4as,7as)-1-hydroxy-7-(hydroxymethyl)-4ah,5h,7ah-cyclopenta[c]pyridine-4-carboxylate)

Structure for NP0229262 (methyl (4as,7as)-1-hydroxy-7-(hydroxymethyl)-4ah,5h,7ah-cyclopenta[c]pyridine-4-carboxylate)

3D Structure for NP0229262 (methyl (4as,7as)-1-hydroxy-7-(hydroxymethyl)-4ah,5h,7ah-cyclopenta[c]pyridine-4-carboxylate)