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Showing NP-Card for saudin (NP0329972)

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Record Information
Version2.0
Created at2022-09-12 14:52:54 UTC
Updated at2022-09-12 14:52:54 UTC
NP-MRD IDNP0329972
Secondary Accession NumbersNone
Natural Product Identification
Common Namesaudin
DescriptionSaudin belongs to the class of organic compounds known as delta valerolactones. These are cyclic organic compounds containing an oxan-2- one moiety. saudin was first documented in 2005 (PMID: 15932211). Based on a literature review a small amount of articles have been published on Saudin (PMID: 32486455) (PMID: 22523435) (PMID: 17064005).
Structure
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MOLSDFPDBSMILESInChI

MOL for NP0329972 (saudin)


  Mrv1652309122216522D          

 27 32  0  0  1  0            999 V2000
    0.9666   -2.2682    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3377   -1.5313    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.9084   -0.7195    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0834   -0.7274    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3255    0.1072    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3140    0.2410    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8004    0.9395    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6097    0.8151    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8588    0.0179    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.4585    0.5845    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6275   -0.2711    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3248    0.1699    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.5585   -1.0958    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.7561   -1.3074    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2437   -0.6315    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2353   -0.8747    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4120   -0.3666    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.9669    0.3280    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1433    0.3761    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0655    1.1743    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6291    1.6194    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2671    1.0964    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4991   -1.0767    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2059   -1.3989    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.6977   -0.6439    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.0991   -1.3647    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7064    0.4412    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  1  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  1  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
  9 10  1  1  0  0  0
  9 11  1  0  0  0  0
 11 12  2  0  0  0  0
 11 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
  9 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  1  0  0  0
 18 19  1  0  0  0  0
 19 20  2  0  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
 18 22  2  0  0  0  0
 17 23  1  0  0  0  0
 24 23  1  1  0  0  0
  2 24  1  0  0  0  0
 24 25  1  0  0  0  0
  6 25  1  0  0  0  0
 15 25  1  0  0  0  0
 25 26  1  6  0  0  0
 17 27  1  0  0  0  0
  6 27  1  0  0  0  0
M  END
Download

3D MOL for NP0329972 (saudin)

Download
3D SDF for NP0329972 (saudin)

  Mrv1652309122216522D          

 27 32  0  0  1  0            999 V2000
    0.9666   -2.2682    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3377   -1.5313    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.9084   -0.7195    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0834   -0.7274    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3255    0.1072    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3140    0.2410    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8004    0.9395    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6097    0.8151    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8588    0.0179    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.4585    0.5845    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6275   -0.2711    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3248    0.1699    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.5585   -1.0958    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.7561   -1.3074    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2437   -0.6315    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2353   -0.8747    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4120   -0.3666    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.9669    0.3280    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1433    0.3761    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0655    1.1743    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6291    1.6194    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2671    1.0964    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4991   -1.0767    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2059   -1.3989    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.6977   -0.6439    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.0991   -1.3647    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7064    0.4412    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  1  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  1  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
  9 10  1  1  0  0  0
  9 11  1  0  0  0  0
 11 12  2  0  0  0  0
 11 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
  9 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  1  0  0  0
 18 19  1  0  0  0  0
 19 20  2  0  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
 18 22  2  0  0  0  0
 17 23  1  0  0  0  0
 24 23  1  1  0  0  0
  2 24  1  0  0  0  0
 24 25  1  0  0  0  0
  6 25  1  0  0  0  0
 15 25  1  0  0  0  0
 25 26  1  6  0  0  0
 17 27  1  0  0  0  0
  6 27  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0329972

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@@H]1[C@@H]2C[C@]3(OC45COC(=O)[C@@]4(C)CCC(OC1=O)(O3)[C@]25C)C1=COC=C1

> <INCHI_IDENTIFIER>
InChI=1S/C20H22O7/c1-11-13-8-18(12-4-7-23-9-12)26-19-10-24-15(22)16(19,2)5-6-20(27-18,17(13,19)3)25-14(11)21/h4,7,9,11,13H,5-6,8,10H2,1-3H3/t11-,13+,16-,17-,18-,19?,20?/m1/s1

> <INCHI_KEY>
MIZCOUBLUGPQEO-FPASHFTESA-N

> <FORMULA>
C20H22O7

> <MOLECULAR_WEIGHT>
374.389

> <EXACT_MASS>
374.136553048

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
49

> <JCHEM_AVERAGE_POLARIZABILITY>
36.69788465620822

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(3R,5S,6R,12S,16R)-3-(furan-3-yl)-6,12,16-trimethyl-2,8,14,17-tetraoxapentacyclo[7.6.1.1^{3,9}.0^{1,12}.0^{5,16}]heptadecane-7,13-dione

> <JCHEM_LOGP>
3.108044123666666

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
6

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
-2.880751763429019

> <JCHEM_POLAR_SURFACE_AREA>
84.20000000000002

> <JCHEM_REFRACTIVITY>
88.8967

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(3R,5S,6R,12S,16R)-3-(furan-3-yl)-6,12,16-trimethyl-2,8,14,17-tetraoxapentacyclo[7.6.1.1^{3,9}.0^{1,12}.0^{5,16}]heptadecane-7,13-dione

> <JCHEM_VEBER_RULE>
0

$$$$

Download
3D-SDF for NP0329972 (saudin)
Download
PDB for NP0329972 (saudin)
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  C   UNK     0       1.804  -4.234   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.497  -2.858   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.696  -1.343   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       0.156  -1.358   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0       2.474   0.200   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       4.319   0.450   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       5.227   1.754   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       6.738   1.522   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       7.203   0.033   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       8.323   1.091   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       8.638  -0.506   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       9.940   0.317   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0       8.509  -2.046   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0       7.011  -2.440   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       6.055  -1.179   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       4.172  -1.633   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0       2.636  -0.684   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       1.805   0.612   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       0.267   0.702   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      -0.122   2.192   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0       1.174   3.023   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0       2.365   2.047   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       2.798  -2.010   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       4.118  -2.611   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       5.036  -1.202   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       5.785  -2.547   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0       3.185   0.824   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   24                                                  
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6                                                       
CONECT    6    5    7   25   27                                             
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10   11   15                                             
CONECT   10    9                                                            
CONECT   11    9   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14    9   16   25                                             
CONECT   16   15   17                                                       
CONECT   17   16   18   23   27                                             
CONECT   18   17   19   22                                                  
CONECT   19   18   20                                                       
CONECT   20   19   21                                                       
CONECT   21   20   22                                                       
CONECT   22   21   18                                                       
CONECT   23   17   24                                                       
CONECT   24   23    2   25                                                  
CONECT   25   24    6   15   26                                             
CONECT   26   25                                                            
CONECT   27   17    6                                                       
MASTER        0    0    0    0    0    0    0    0   27    0   64    0
END

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3D PDB for NP0329972 (saudin)
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SMILES for NP0329972 (saudin)
C[C@@H]1[C@@H]2C[C@]3(OC45COC(=O)[C@@]4(C)CCC(OC1=O)(O3)[C@]25C)C1=COC=C1
Download
INCHI for NP0329972 (saudin)
InChI=1S/C20H22O7/c1-11-13-8-18(12-4-7-23-9-12)26-19-10-24-15(22)16(19,2)5-6-20(27-18,17(13,19)3)25-14(11)21/h4,7,9,11,13H,5-6,8,10H2,1-3H3/t11-,13+,16-,17-,18-,19?,20?/m1/s1
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SynonymsNot Available
Chemical FormulaC20H22O7
Average Mass374.3890 Da
Monoisotopic Mass374.13655 Da
IUPAC Name(3R,5S,6R,12S,16R)-3-(furan-3-yl)-6,12,16-trimethyl-2,8,14,17-tetraoxapentacyclo[7.6.1.1^{3,9}.0^{1,12}.0^{5,16}]heptadecane-7,13-dione
Traditional Name(3R,5S,6R,12S,16R)-3-(furan-3-yl)-6,12,16-trimethyl-2,8,14,17-tetraoxapentacyclo[7.6.1.1^{3,9}.0^{1,12}.0^{5,16}]heptadecane-7,13-dione
CAS Registry NumberNot Available
SMILES
C[C@@H]1[C@@H]2C[C@]3(OC45COC(=O)[C@@]4(C)CCC(OC1=O)(O3)[C@]25C)C1=COC=C1
InChI Identifier
InChI=1S/C20H22O7/c1-11-13-8-18(12-4-7-23-9-12)26-19-10-24-15(22)16(19,2)5-6-20(27-18,17(13,19)3)25-14(11)21/h4,7,9,11,13H,5-6,8,10H2,1-3H3/t11-,13+,16-,17-,18-,19?,20?/m1/s1
InChI KeyMIZCOUBLUGPQEO-FPASHFTESA-N
Experimental Spectra
Not Available
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of OriginNot Available
Chemical Taxonomy
Description Belongs to the class of organic compounds known as delta valerolactones. These are cyclic organic compounds containing an oxan-2- one moiety.
KingdomOrganic compounds  
Super ClassOrganoheterocyclic compounds  
ClassLactones  
Sub ClassDelta valerolactones  
Direct ParentDelta valerolactones  
Alternative Parents
Substituents
  • Ketal
    • 

  • Delta valerolactone
    • 

  • Delta_valerolactone
    • 

  • Meta-dioxane
    • 

  • Dicarboxylic acid or derivatives
    • 

  • Gamma butyrolactone
    • 

  • Oxane
    • 

  • Furan
    • 

  • Heteroaromatic compound
    • 

  • Oxolane
    • 

  • Carboxylic acid ester
    • 

  • Acetal
    • 

  • Carboxylic acid derivative
    • 

  • Oxacycle
    • 

  • Organic oxygen compound
    • 

  • Hydrocarbon derivative
    • 

  • Organic oxide
    • 

  • Carbonyl group
    • 

  • Organooxygen compound
    • 

  • 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
logP3.11ChemAxon
pKa (Strongest Basic)-2.9ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area84.2 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity88.9 m³·mol⁻¹ChemAxon
Polarizability36.7 ųChemAxon
Number of Rings6ChemAxon
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 IDC00040808  
Chemspider ID2343039  
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkSaudin  
METLIN IDNot Available
PubChem Compound3086407  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. Elfaky MA, El-Halawany AM, Koshak AE, Alshali KZ, El-Araby ME, Khayat MT, Abdallah HM: Bioassay Guided Isolation and Docking Studies of a Potential beta-Lactamase Inhibitor from Clutia myricoides. Molecules. 2020 May 31;25(11). pii: molecules25112566. doi: 10.3390/molecules25112566. [PubMed:32486455  ] 
  2. Boeckman RK Jr, Del Rosario Ferreira MR, Mitchell LH, Shao P, Neeb MJ, Fang Y: Studies Culminating in the Total Synthesis and Determination of the Absolute Configuration of (-)-Saudin. Tetrahedron. 2011 Dec 23;67(51):9787-9808. doi: 10.1016/j.tet.2011.09.067. Epub 2011 Sep 21. [PubMed:22523435  ] 
  3. Tambar UK, Kano T, Zepernick JF, Stoltz BM: Convergent and diastereoselective synthesis of the polycyclic pyran core of saudin. J Org Chem. 2006 Oct 27;71(22):8357-64. doi: 10.1021/jo061236+. [PubMed:17064005  ] 
  4. Tambar UK, Kano T, Stoltz BM: Progress toward the total synthesis of saudin: development of a tandem Stille-oxa-electrocyclization reaction. Org Lett. 2005 Jun 9;7(12):2413-6. doi: 10.1021/ol050705b. [PubMed:15932211  ] 
  5. LOTUS database [Link]