NP-MRD: Showing NP-Card for (3'r,4r)-1,3'-dihydroxyspiro[2,7-naphthyridine-4,1'-cyclopentan]-3-one (NP0330254)

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Record Information

Version

1.0

Created at

2022-09-12 15:25:26 UTC

Updated at

2022-09-12 15:25:26 UTC

NP-MRD ID

NP0330254

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(3'r,4r)-1,3'-dihydroxyspiro[2,7-naphthyridine-4,1'-cyclopentan]-3-one

Description

Sesbanine belongs to the class of organic compounds known as naphthyridines. Naphthyridines are compounds containing a naphthyridine moiety, a naphthalene in which a carbon atom has been replaced by a nitrogen in each of the two rings. The naphthyridine skeleton can also be described as an assembly two fused pyridine rings, which do not share their nitrogen atom. (3'r,4r)-1,3'-dihydroxyspiro[2,7-naphthyridine-4,1'-cyclopentan]-3-one is found in Sesbania drummondii. It was first documented in 2022 (PMID: 36130844). Based on a literature review a significant number of articles have been published on Sesbanine (PMID: 36130843) (PMID: 36130842) (PMID: 36130841) (PMID: 36130840).

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 29 31  0  0  0  0  0  0  0  0999 V2000
   -1.4852    1.0830   -2.1968 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3834    0.8571   -1.5660 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8168    1.4177   -2.0469 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.9716    1.2715   -1.5168 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1298    1.8279   -2.0032 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0381    0.4390   -0.2931 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2792    0.2640    0.3025 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3976   -0.4802    1.4128 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.3120   -1.0582    1.9504 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0822   -0.9046    1.3889 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9193   -0.1380    0.2340 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3945    0.0240   -0.3628 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.1175   -1.2911   -0.5789 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5993   -0.9462   -0.4839 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6818    0.3769    0.2316 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.5222    0.3005    1.3528 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2935    0.7351    0.6726 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9700    1.3392   -2.2408 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1442    0.7396   -0.1477 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4003   -1.6659    2.8547 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2104   -1.3781    1.8342 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8856   -1.9832    0.2231 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8611   -1.7640   -1.5449 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0405   -0.9105   -1.5089 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1705   -1.6915    0.0869 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0813    1.1321   -0.4894 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9609    0.2150    2.1525 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1263    1.8253    0.5964 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0682    0.3637    1.6865 H   0  0  0  0  0  0  0  0  0  0  0  0
 16 15  1  0
 15 14  1  0
 14 13  1  0
 13 12  1  0
 12 17  1  0
 12  2  1  6
  2  1  2  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  4  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  2  0
  9 10  1  0
 10 11  2  0
 17 15  1  0
 11  6  1  0
 11 12  1  0
 16 27  1  0
 15 26  1  6
 14 24  1  0
 14 25  1  0
 13 22  1  0
 13 23  1  0
 17 28  1  0
 17 29  1  0
  5 18  1  0
  7 19  1  0
  9 20  1  0
 10 21  1  0
M  END


  Mrv1652309122217252D          

 17 19  0  0  1  0            999 V2000
    2.2871    1.4612    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0765    1.2215    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6789    1.7852    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.4683    1.5454    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0706    2.1092    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.6553    0.7419    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4447    0.5021    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6317   -0.3014    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.0294   -0.8651    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2400   -0.6253    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0530    0.1782    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2636    0.4179    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.3656   -0.4007    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6185   -0.7507    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0548   -0.1484    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.2361   -0.2504    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4534    0.5739    0.0000 C   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  2  0  0  0  0
  4  5  1  0  0  0  0
  4  6  1  0  0  0  0
  6  7  2  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  9 10  1  0  0  0  0
 10 11  2  0  0  0  0
  6 11  1  0  0  0  0
 11 12  1  0  0  0  0
  2 12  1  0  0  0  0
 12 13  1  6  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  1  0  0  0
 15 17  1  0  0  0  0
 12 17  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0330254

> <DATABASE_NAME>
NP-MRD

> <SMILES>
O[C@@H]1CC[C@]2(C1)C(=O)N=C(O)C1=CN=CC=C21

> <INCHI_IDENTIFIER>
InChI=1S/C12H12N2O3/c15-7-1-3-12(5-7)9-2-4-13-6-8(9)10(16)14-11(12)17/h2,4,6-7,15H,1,3,5H2,(H,14,16,17)/t7-,12-/m1/s1

> <INCHI_KEY>
UETOAKFPMASNTK-JMCQJSRRSA-N

> <FORMULA>
C12H12N2O3

> <MOLECULAR_WEIGHT>
232.239

> <EXACT_MASS>
232.084792254

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
29

> <JCHEM_AVERAGE_POLARIZABILITY>
22.661701960732124

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(3'R,4R)-1,3'-dihydroxy-3H-spiro[2,7-naphthyridine-4,1'-cyclopentane]-3-one

> <JCHEM_LOGP>
-0.03888972233333323

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
15.226015981710901

> <JCHEM_PKA_STRONGEST_ACIDIC>
6.601650946848588

> <JCHEM_PKA_STRONGEST_BASIC>
3.737052018679656

> <JCHEM_POLAR_SURFACE_AREA>
82.78

> <JCHEM_REFRACTIVITY>
59.6758

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(3'R,4R)-1,3'-dihydroxyspiro[2,7-naphthyridine-4,1'-cyclopentane]-3-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 12-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   12-SEP-22         0                                  
HETATM    1  O   UNK     0       4.269   2.728   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       5.743   2.280   0.000  0.00  0.00           C+0
HETATM    3  N   UNK     0       6.867   3.332   0.000  0.00  0.00           N+0
HETATM    4  C   UNK     0       8.341   2.885   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       9.465   3.937   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       8.690   1.385   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      10.163   0.937   0.000  0.00  0.00           C+0
HETATM    8  N   UNK     0      10.513  -0.563   0.000  0.00  0.00           N+0
HETATM    9  C   UNK     0       9.388  -1.615   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       7.915  -1.167   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       7.566   0.333   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       6.092   0.780   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       6.282  -0.748   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       4.888  -1.401   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       3.836  -0.277   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       2.307  -0.467   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0       4.580   1.071   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3   12                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4    7   11                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10    6   12                                                  
CONECT   12   11    2   13   17                                             
CONECT   13   12   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   16   17                                                  
CONECT   16   15                                                            
CONECT   17   15   12                                                       
MASTER        0    0    0    0    0    0    0    0   17    0   38    0
END

View in JSmol

Synonyms

Value	Source
Sesbanine, cis-(+-)-isomer	MeSH
Sesbanine, trans-(+-)-isomer	MeSH

Chemical Formula

C₁₂H₁₂N₂O₃

Average Mass

232.2390 Da

Monoisotopic Mass

232.08479 Da

IUPAC Name

Not Available

Traditional Name

Not Available

CAS Registry Number

Not Available

SMILES

O[C@@H]1CC[C@]2(C1)C(=O)N=C(O)C1=CN=CC=C21

InChI Identifier

InChI=1S/C12H12N2O3/c15-7-1-3-12(5-7)9-2-4-13-6-8(9)10(16)14-11(12)17/h2,4,6-7,15H,1,3,5H2,(H,14,16,17)/t7-,12-/m1/s1

InChI Key

UETOAKFPMASNTK-JMCQJSRRSA-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
Sesbania drummondii	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as naphthyridines. Naphthyridines are compounds containing a naphthyridine moiety, a naphthalene in which a carbon atom has been replaced by a nitrogen in each of the two rings. The naphthyridine skeleton can also be described as an assembly two fused pyridine rings, which do not share their nitrogen atom.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Diazanaphthalenes

Sub Class

Naphthyridines

Direct Parent

Naphthyridines

Alternative Parents

Substituents

Naphthyridine
Pyridine
Carboxylic acid imide
Cyclic alcohol
Dicarboximide
Carboxylic acid imide, n-unsubstituted
Heteroaromatic compound
Secondary alcohol
Carboxylic acid derivative
Azacycle
Alcohol
Organonitrogen compound
Organooxygen compound
Hydrocarbon derivative
Organic oxide
Organopnictogen compound
Organic oxygen compound
Organic nitrogen compound
Carbonyl group
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

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

293644

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

331428

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Cani I, Righini M, Cenni P, Foschi M: Teaching NeuroImage: Partially Reversible Widespread Leukoencephalopathy Associated With Atypical Hemolytic Uremic Syndrome. Neurology. 2022 Sep 21. pii: WNL.0000000000201378. doi: 10.1212/WNL.0000000000201378. [PubMed:36130844 ]
Sasaki R, Morimoto S, Ozawa F, Okano H, Yoshida M, Ishiura H, Tsuji S, Kuzuhara S, Kokubo Y: APOE Alleles With Tau and Abeta Pathology In Patients With Amyotrophic Lateral Sclerosis and Parkinsonism-Dementia Complex in the Kii Peninsula. Neurology. 2022 Sep 21. pii: WNL.0000000000201156. doi: 10.1212/WNL.0000000000201156. [PubMed:36130843 ]
Zhang Z, Wang M, Gill D, Liu X: Genetically Predicted Smoking and Alcohol Consumption and Functional Outcome After Ischemic Stroke. Neurology. 2022 Sep 21. pii: WNL.0000000000201291. doi: 10.1212/WNL.0000000000201291. [PubMed:36130842 ]
Khamis S, Mitakidou MR, Champion M, Goyal S, Jones RL, Siddiqui A, Sabanathan S, Hedderly T, Lin JP, Jungbluth H, Papandreou A: Clinical Reasoning: A Teenage Girl With Progressive Hyperkinetic Movements, Seizures, and Encephalopathy. Neurology. 2022 Sep 21. pii: WNL.0000000000201385. doi: 10.1212/WNL.0000000000201385. [PubMed:36130841 ]
Rosenberg A, Ohlund-Wistbacka U, Hall A, Bonnard A, Hagman G, Ryden M, Thunborg C, Wiggenraad F, Sandebring-Matton A, Solomon A, Kivipelto M: beta-Amyloid, Tau, Neurodegeneration Classification and Eligibility for Anti-amyloid Treatment in a Memory Clinic Population. Neurology. 2022 Sep 21. pii: WNL.0000000000201043. doi: 10.1212/WNL.0000000000201043. [PubMed:36130840 ]
LOTUS database [Link]

Showing NP-Card for (3'r,4r)-1,3'-dihydroxyspiro[2,7-naphthyridine-4,1'-cyclopentan]-3-one (NP0330254)

MOL for NP0330254 ((3'r,4r)-1,3'-dihydroxyspiro[2,7-naphthyridine-4,1'-cyclopentan]-3-one)

3D MOL for NP0330254 ((3'r,4r)-1,3'-dihydroxyspiro[2,7-naphthyridine-4,1'-cyclopentan]-3-one)

3D SDF for NP0330254 ((3'r,4r)-1,3'-dihydroxyspiro[2,7-naphthyridine-4,1'-cyclopentan]-3-one)

3D-SDF for NP0330254 ((3'r,4r)-1,3'-dihydroxyspiro[2,7-naphthyridine-4,1'-cyclopentan]-3-one)

PDB for NP0330254 ((3'r,4r)-1,3'-dihydroxyspiro[2,7-naphthyridine-4,1'-cyclopentan]-3-one)

3D PDB for NP0330254 ((3'r,4r)-1,3'-dihydroxyspiro[2,7-naphthyridine-4,1'-cyclopentan]-3-one)

SMILES for NP0330254 ((3'r,4r)-1,3'-dihydroxyspiro[2,7-naphthyridine-4,1'-cyclopentan]-3-one)

INCHI for NP0330254 ((3'r,4r)-1,3'-dihydroxyspiro[2,7-naphthyridine-4,1'-cyclopentan]-3-one)

Structure for NP0330254 ((3'r,4r)-1,3'-dihydroxyspiro[2,7-naphthyridine-4,1'-cyclopentan]-3-one)

3D Structure for NP0330254 ((3'r,4r)-1,3'-dihydroxyspiro[2,7-naphthyridine-4,1'-cyclopentan]-3-one)