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Showing NP-Card for Nagilactone D (NP0050250)

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Record Information
Version2.0
Created at2022-04-27 20:49:56 UTC
Updated at2022-04-27 20:49:56 UTC
NP-MRD IDNP0050250
Secondary Accession NumbersNone
Natural Product Identification
Common NameNagilactone D
DescriptionNagilactone D belongs to the class of organic compounds known as naphthopyrans. Naphthopyrans are compounds containing a pyran ring fused to a naphthalene moiety. Furan is a 6 membered-ring non-aromatic ring with five carbon and one oxygen atoms. Naphthalene is a polycyclic aromatic hydrocarbon made up of two fused benzene rings. Nagilactone D is found in Afrocarpus gracilior, Myrica nagi , Podocarpus nagi and Nageia wallichiana. Nagilactone D was first documented in 2015 (PMID: 25807242). Based on a literature review very few articles have been published on Nagilactone D (PMID: 31953203).
Structure
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MOLSDFPDBSMILESInChI

MOL for NP0050250 (Nagilactone D)


  Mrv1652304272222492D          

 24 28  0  0  1  0            999 V2000
    2.1266   -0.4952    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.1042    0.3295    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.8073    0.7612    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.9569    1.5725    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3885    2.1704    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.7748    1.6809    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1306    0.9366    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.9218    0.7030    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1151   -0.0991    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5172   -0.6675    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5550   -0.4565    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.8519   -0.8882    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.1489   -1.3199    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5327    0.3682    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.6925   -1.2700    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7105   -1.4695    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5017   -1.7032    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6950   -2.5052    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.0997   -1.1347    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.9064   -0.3327    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.5043    0.2357    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.2955    0.0021    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1270    1.2279    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3789    0.7225    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
  4  5  2  0  0  0  0
  4  6  1  0  0  0  0
  7  6  1  6  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
  1 12  1  0  0  0  0
 12 13  1  6  0  0  0
  1 13  1  6  0  0  0
 11 14  1  0  0  0  0
 14  3  1  6  0  0  0
  7 14  1  0  0  0  0
 11 15  1  6  0  0  0
 10 16  2  0  0  0  0
 16 17  1  0  0  0  0
 17 18  2  0  0  0  0
 17 19  1  0  0  0  0
 19 20  1  0  0  0  0
  9 20  2  0  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
  3 23  1  1  0  0  0
  2 24  1  6  0  0  0
M  END
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3D MOL for NP0050250 (Nagilactone D)

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3D SDF for NP0050250 (Nagilactone D)

  Mrv1652304272222492D          

 24 28  0  0  1  0            999 V2000
    2.1266   -0.4952    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.1042    0.3295    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.8073    0.7612    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.9569    1.5725    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3885    2.1704    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.7748    1.6809    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1306    0.9366    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.9218    0.7030    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1151   -0.0991    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5172   -0.6675    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5550   -0.4565    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.8519   -0.8882    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.1489   -1.3199    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5327    0.3682    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.6925   -1.2700    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7105   -1.4695    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5017   -1.7032    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6950   -2.5052    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.0997   -1.1347    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.9064   -0.3327    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.5043    0.2357    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.2955    0.0021    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1270    1.2279    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3789    0.7225    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
  4  5  2  0  0  0  0
  4  6  1  0  0  0  0
  7  6  1  6  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
  1 12  1  0  0  0  0
 12 13  1  6  0  0  0
  1 13  1  6  0  0  0
 11 14  1  0  0  0  0
 14  3  1  6  0  0  0
  7 14  1  0  0  0  0
 11 15  1  6  0  0  0
 10 16  2  0  0  0  0
 16 17  1  0  0  0  0
 17 18  2  0  0  0  0
 17 19  1  0  0  0  0
 19 20  1  0  0  0  0
  9 20  2  0  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
  3 23  1  1  0  0  0
  2 24  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0050250

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CCC1=C2C[C@H]3OC(=O)[C@]4(C)[C@H]3[C@](C)([C@@H]3O[C@@H]3[C@@H]4O)C2=CC(=O)O1

> <INCHI_IDENTIFIER>
InChI=1S/C18H20O6/c1-4-9-7-5-10-13-17(2,8(7)6-11(19)22-9)15-12(24-15)14(20)18(13,3)16(21)23-10/h6,10,12-15,20H,4-5H2,1-3H3/t10-,12-,13-,14+,15-,17-,18-/m1/s1

> <INCHI_KEY>
UEZYUDAMQBJVJP-CQVMLLNQSA-N

> <FORMULA>
C18H20O6

> <MOLECULAR_WEIGHT>
332.352

> <EXACT_MASS>
332.125988364

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
44

> <JCHEM_AVERAGE_POLARIZABILITY>
33.22966501695626

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(1S,2S,4R,5R,6R,9R,17R)-12-ethyl-5-hydroxy-1,6-dimethyl-3,8,13-trioxapentacyclo[7.7.1.0^{2,4}.0^{6,17}.0^{11,16}]heptadeca-11,15-diene-7,14-dione

> <ALOGPS_LOGP>
1.88

> <JCHEM_LOGP>
0.753706215333334

> <ALOGPS_LOGS>
-2.26

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.41298224905358

> <JCHEM_PKA_STRONGEST_BASIC>
-3.4929615642639638

> <JCHEM_POLAR_SURFACE_AREA>
85.36

> <JCHEM_REFRACTIVITY>
82.79009999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.84e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1S,2S,4R,5R,6R,9R,17R)-12-ethyl-5-hydroxy-1,6-dimethyl-3,8,13-trioxapentacyclo[7.7.1.0^{2,4}.0^{6,17}.0^{11,16}]heptadeca-11,15-diene-7,14-dione

> <JCHEM_VEBER_RULE>
0

$$$$

Download
3D-SDF for NP0050250 (Nagilactone D)
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PDB for NP0050250 (Nagilactone D)
HEADER    PROTEIN                                 27-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   27-APR-22         0                                  
HETATM    1  C   UNK     0       3.970  -0.924   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       3.928   0.615   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       5.240   1.421   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       5.520   2.935   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       4.459   4.051   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0       7.046   3.138   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0       7.710   1.748   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       9.187   1.312   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       9.548  -0.185   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       8.432  -1.246   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       6.636  -0.852   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       5.324  -1.658   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       4.011  -2.464   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0       6.594   0.687   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       6.893  -2.371   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       8.793  -2.743   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      10.270  -3.179   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0      10.631  -4.676   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0      11.386  -2.118   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0      11.025  -0.621   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      12.141   0.440   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      13.618   0.004   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       3.970   2.292   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0       2.574   1.349   0.000  0.00  0.00           O+0
CONECT    1    2   12   13                                                  
CONECT    2    1    3   24                                                  
CONECT    3    2    4   14   23                                             
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4    7                                                       
CONECT    7    6    8   14                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10   20                                                  
CONECT   10    9   11   16                                                  
CONECT   11   10   12   14   15                                             
CONECT   12   11    1   13                                                  
CONECT   13   12    1                                                       
CONECT   14   11    3    7                                                  
CONECT   15   11                                                            
CONECT   16   10   17                                                       
CONECT   17   16   18   19                                                  
CONECT   18   17                                                            
CONECT   19   17   20                                                       
CONECT   20   19    9   21                                                  
CONECT   21   20   22                                                       
CONECT   22   21                                                            
CONECT   23    3                                                            
CONECT   24    2                                                            
MASTER        0    0    0    0    0    0    0    0   24    0   56    0
END

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3D PDB for NP0050250 (Nagilactone D)
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SMILES for NP0050250 (Nagilactone D)
CCC1=C2C[C@H]3OC(=O)[C@]4(C)[C@H]3[C@](C)([C@@H]3O[C@@H]3[C@@H]4O)C2=CC(=O)O1
Download
INCHI for NP0050250 (Nagilactone D)
InChI=1S/C18H20O6/c1-4-9-7-5-10-13-17(2,8(7)6-11(19)22-9)15-12(24-15)14(20)18(13,3)16(21)23-10/h6,10,12-15,20H,4-5H2,1-3H3/t10-,12-,13-,14+,15-,17-,18-/m1/s1
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View in JSmol
SynonymsNot Available
Chemical FormulaC18H20O6
Average Mass332.3520 Da
Monoisotopic Mass332.12599 Da
IUPAC Name(1S,2S,4R,5R,6R,9R,17R)-12-ethyl-5-hydroxy-1,6-dimethyl-3,8,13-trioxapentacyclo[7.7.1.0^{2,4}.0^{6,17}.0^{11,16}]heptadeca-11,15-diene-7,14-dione
Traditional Name(1S,2S,4R,5R,6R,9R,17R)-12-ethyl-5-hydroxy-1,6-dimethyl-3,8,13-trioxapentacyclo[7.7.1.0^{2,4}.0^{6,17}.0^{11,16}]heptadeca-11,15-diene-7,14-dione
CAS Registry NumberNot Available
SMILES
CCC1=C2C[C@H]3OC(=O)[C@]4(C)[C@H]3[C@](C)([C@@H]3O[C@@H]3[C@@H]4O)C2=CC(=O)O1
InChI Identifier
InChI=1S/C18H20O6/c1-4-9-7-5-10-13-17(2,8(7)6-11(19)22-9)15-12(24-15)14(20)18(13,3)16(21)23-10/h6,10,12-15,20H,4-5H2,1-3H3/t10-,12-,13-,14+,15-,17-,18-/m1/s1
InChI KeyUEZYUDAMQBJVJP-CQVMLLNQSA-N
Experimental Spectra
Not Available
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Afrocarpus graciliorLOTUS Database
Myrica nagiPlant
Nageia nagiPlant
Nageia wallichianaLOTUS Database
Chemical Taxonomy
Description Belongs to the class of organic compounds known as naphthopyrans. Naphthopyrans are compounds containing a pyran ring fused to a naphthalene moiety. Furan is a 6 membered-ring non-aromatic ring with five carbon and one oxygen atoms. Naphthalene is a polycyclic aromatic hydrocarbon  made up of two fused benzene rings.
KingdomOrganic compounds  
Super ClassOrganoheterocyclic compounds  
ClassNaphthopyrans  
Sub ClassNot Available
Direct ParentNaphthopyrans  
Alternative Parents
Substituents
  • Naphthopyran
    • 

  • Naphthalene
    • 

  • Oxepane
    • 

  • Pyranone
    • 

  • Gamma butyrolactone
    • 

  • Pyran
    • 

  • Cyclic alcohol
    • 

  • Heteroaromatic compound
    • 

  • Tetrahydrofuran
    • 

  • Carboxylic acid ester
    • 

  • Lactone
    • 

  • Secondary alcohol
    • 

  • Monocarboxylic acid or derivatives
    • 

  • Ether
    • 

  • Oxirane
    • 

  • Dialkyl ether
    • 

  • Carboxylic acid derivative
    • 

  • Oxacycle
    • 

  • Hydrocarbon derivative
    • 

  • Organic oxide
    • 

  • Organic oxygen compound
    • 

  • Alcohol
    • 

  • Organooxygen compound
    • 

  • Carbonyl group
    • 

  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External DescriptorsNot Available
Physical Properties
StateNot Available
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP1.88ALOGPS
logP0.75ChemAxon
logS-2.3ALOGPS
pKa (Strongest Acidic)13.41ChemAxon
pKa (Strongest Basic)-3.5ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area85.36 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity82.79 m³·mol⁻¹ChemAxon
Polarizability33.23 ųChemAxon
Number of Rings5ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDNot Available
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDC00000271  
Chemspider ID2341412  
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound3084330  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. Li A, Xiao X, Feng ZL, Chen X, Liu LJ, Lin LG, Lu JJ, Zhang LL: Nagilactone D ameliorates experimental pulmonary fibrosis in vitro and in vivo via modulating TGF-beta/Smad signaling pathway. Toxicol Appl Pharmacol. 2020 Jan 15;389:114882. doi: 10.1016/j.taap.2020.114882.  Epub 2020 Jan 15. [PubMed:31953203  ] 
  2. Addo EM, Chai HB, Hymete A, Yeshak MY, Slebodnick C, Kingston DG, Rakotondraibe LH: Antiproliferative Constituents of the Roots of Ethiopian Podocarpus falcatus and Structure Revision of 2alpha-Hydroxynagilactone F and Nagilactone I. J Nat Prod. 2015 Apr 24;78(4):827-35. doi: 10.1021/np501062f. Epub 2015 Mar 25. [PubMed:25807242  ]