NP-MRD: Showing NP-Card for Depudecin (NP0005176)

Jump To Section:

Identification Spectra BioTaxonomy ChemoTaxonomy Physical properties Links References XML

Record Information

Version

2.0

Created at

2020-12-09 02:30:01 UTC

Updated at

2021-07-15 16:51:15 UTC

NP-MRD ID

NP0005176

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Depudecin

Provided By

NPAtlas

Description

Depudecin is a secondary metabolite. Secondary metabolites are metabolically or physiologically non-essential metabolites that may serve a role as defense or signalling molecules. In some cases they are simply molecules that arise from the incomplete metabolism of other secondary metabolites. Depudecin is found in Alternaria brassicicola. Depudecin was first documented in 1992 (PMID: 1500354). Based on a literature review a small amount of articles have been published on depudecin (PMID: 10737176) (PMID: 11562279) (PMID: 12623206) (PMID: 1731795).

Structure

MOL 3D MOL SDF 3D SDF PDB SMILES InChI


  Mrv1652306242118173D          

 31 32  0  0  0  0            999 V2000
    5.8068   -0.6368    0.4829 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6085   -0.5868   -0.0603 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9310    0.7357   -0.1711 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.2008    1.2302   -1.4380 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4475    0.6507    0.0157 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.9327    0.1796    1.2172 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7389   -0.6037    0.0279 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.3580   -0.6284   -0.5144 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6613   -0.4073    0.2731 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0473   -0.4379   -0.2998 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.5551    0.8122   -0.6998 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0897    0.2014    0.4965 C   0  0  1  0  0  0  0  0  0  0  0  0
   -4.5295   -0.2526    0.3817 C   0  0  1  0  0  0  0  0  0  0  0  0
   -5.3463    0.9664    0.0055 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6104   -1.1870   -0.6354 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.3528   -1.5866    0.5898 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.3110    0.2471    0.8487 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1592   -1.5000   -0.4053 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3229    1.4594    0.5658 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5176    1.8617   -1.7599 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9017    1.5500   -0.3581 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1949   -1.5871    0.1360 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2285   -0.8335   -1.5714 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5185   -0.2021    1.3347 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3112   -1.3313   -0.9006 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7850    0.8055    1.3862 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8122   -0.6916    1.3384 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5949    1.4890    0.9480 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2595    0.6677   -0.5557 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7060    1.6598   -0.5944 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1858   -2.0437   -0.3625 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  3  0  0  0
  2  3  1  0  0  0  0
  3  4  1  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  2  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
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 13 15  1  0  0  0  0
  7  5  1  0  0  0  0
 12 10  1  0  0  0  0
  1 16  1  0  0  0  0
  1 17  1  0  0  0  0
  2 18  1  0  0  0  0
  3 19  1  1  0  0  0
  4 20  1  0  0  0  0
  5 21  1  6  0  0  0
  7 22  1  1  0  0  0
  8 23  1  0  0  0  0
  9 24  1  0  0  0  0
 10 25  1  6  0  0  0
 12 26  1  1  0  0  0
 13 27  1  1  0  0  0
 14 28  1  0  0  0  0
 14 29  1  0  0  0  0
 14 30  1  0  0  0  0
 15 31  1  0  0  0  0
M  END

     RDKit          3D

 31 32  0  0  0  0  0  0  0  0999 V2000
    5.8068   -0.6368    0.4829 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6085   -0.5868   -0.0603 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9310    0.7357   -0.1711 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.2008    1.2302   -1.4380 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4475    0.6507    0.0157 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.9327    0.1796    1.2172 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7389   -0.6037    0.0279 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.3580   -0.6284   -0.5144 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6613   -0.4073    0.2731 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0473   -0.4379   -0.2998 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.5551    0.8122   -0.6998 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0897    0.2014    0.4965 C   0  0  1  0  0  0  0  0  0  0  0  0
   -4.5295   -0.2526    0.3817 C   0  0  1  0  0  0  0  0  0  0  0  0
   -5.3463    0.9664    0.0055 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6104   -1.1870   -0.6354 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.3528   -1.5866    0.5898 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.3110    0.2471    0.8487 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1592   -1.5000   -0.4053 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3229    1.4594    0.5658 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5176    1.8617   -1.7599 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9017    1.5500   -0.3581 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1949   -1.5871    0.1360 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2285   -0.8335   -1.5714 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5185   -0.2021    1.3347 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3112   -1.3313   -0.9006 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7850    0.8055    1.3862 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8122   -0.6916    1.3384 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5949    1.4890    0.9480 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2595    0.6677   -0.5557 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7060    1.6598   -0.5944 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1858   -2.0437   -0.3625 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  3
  2  3  1  0
  3  4  1  0
  3  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  2  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 13 15  1  0
  7  5  1  0
 12 10  1  0
  1 16  1  0
  1 17  1  0
  2 18  1  0
  3 19  1  1
  4 20  1  0
  5 21  1  6
  7 22  1  1
  8 23  1  0
  9 24  1  0
 10 25  1  6
 12 26  1  1
 13 27  1  1
 14 28  1  0
 14 29  1  0
 14 30  1  0
 15 31  1  0
M  END


  Mrv1652306242118173D          

 31 32  0  0  0  0            999 V2000
    5.8068   -0.6368    0.4829 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6085   -0.5868   -0.0603 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9310    0.7357   -0.1711 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.2008    1.2302   -1.4380 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4475    0.6507    0.0157 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.9327    0.1796    1.2172 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7389   -0.6037    0.0279 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.3580   -0.6284   -0.5144 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6613   -0.4073    0.2731 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0473   -0.4379   -0.2998 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.5551    0.8122   -0.6998 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0897    0.2014    0.4965 C   0  0  1  0  0  0  0  0  0  0  0  0
   -4.5295   -0.2526    0.3817 C   0  0  1  0  0  0  0  0  0  0  0  0
   -5.3463    0.9664    0.0055 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6104   -1.1870   -0.6354 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.3528   -1.5866    0.5898 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.3110    0.2471    0.8487 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1592   -1.5000   -0.4053 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3229    1.4594    0.5658 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5176    1.8617   -1.7599 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9017    1.5500   -0.3581 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1949   -1.5871    0.1360 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2285   -0.8335   -1.5714 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5185   -0.2021    1.3347 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3112   -1.3313   -0.9006 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7850    0.8055    1.3862 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8122   -0.6916    1.3384 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5949    1.4890    0.9480 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2595    0.6677   -0.5557 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7060    1.6598   -0.5944 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1858   -2.0437   -0.3625 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  3  0  0  0
  2  3  1  0  0  0  0
  3  4  1  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  2  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
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 13 15  1  0  0  0  0
  7  5  1  0  0  0  0
 12 10  1  0  0  0  0
  1 16  1  0  0  0  0
  1 17  1  0  0  0  0
  2 18  1  0  0  0  0
  3 19  1  1  0  0  0
  4 20  1  0  0  0  0
  5 21  1  6  0  0  0
  7 22  1  1  0  0  0
  8 23  1  0  0  0  0
  9 24  1  0  0  0  0
 10 25  1  6  0  0  0
 12 26  1  1  0  0  0
 13 27  1  1  0  0  0
 14 28  1  0  0  0  0
 14 29  1  0  0  0  0
 14 30  1  0  0  0  0
 15 31  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0005176

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H]O[C@]([H])(C([H])=C([H])[H])[C@]1([H])O[C@@]1([H])C(\[H])=C(/[H])[C@]1([H])O[C@@]1([H])[C@]([H])(O[H])C([H])([H])[H]

> <INCHI_IDENTIFIER>
InChI=1S/C11H16O4/c1-3-7(13)11-9(15-11)5-4-8-10(14-8)6(2)12/h3-13H,1H2,2H3/b5-4+/t6-,7-,8+,9+,10+,11+/m1/s1

> <INCHI_KEY>
DLVJMFOLJOOWFS-INMLLLKOSA-N

> <FORMULA>
C11H16O4

> <MOLECULAR_WEIGHT>
212.245

> <EXACT_MASS>
212.104858995

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
31

> <JCHEM_AVERAGE_POLARIZABILITY>
22.626635429968758

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(1R)-1-[(2S,3S)-3-[(E)-2-[(2S,3S)-3-[(1R)-1-hydroxyethyl]oxiran-2-yl]ethenyl]oxiran-2-yl]prop-2-en-1-ol

> <ALOGPS_LOGP>
-0.27

> <JCHEM_LOGP>
0.32819588733333255

> <ALOGPS_LOGS>
-0.84

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.496781675922652

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.665458055685782

> <JCHEM_PKA_STRONGEST_BASIC>
-3.0565551286220156

> <JCHEM_POLAR_SURFACE_AREA>
65.52

> <JCHEM_REFRACTIVITY>
54.953700000000005

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.04e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
depudecin

> <JCHEM_VEBER_RULE>
0

$$$$

     RDKit          3D

 31 32  0  0  0  0  0  0  0  0999 V2000
    5.8068   -0.6368    0.4829 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6085   -0.5868   -0.0603 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9310    0.7357   -0.1711 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.2008    1.2302   -1.4380 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4475    0.6507    0.0157 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.9327    0.1796    1.2172 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7389   -0.6037    0.0279 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.3580   -0.6284   -0.5144 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6613   -0.4073    0.2731 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0473   -0.4379   -0.2998 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.5551    0.8122   -0.6998 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0897    0.2014    0.4965 C   0  0  1  0  0  0  0  0  0  0  0  0
   -4.5295   -0.2526    0.3817 C   0  0  1  0  0  0  0  0  0  0  0  0
   -5.3463    0.9664    0.0055 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6104   -1.1870   -0.6354 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.3528   -1.5866    0.5898 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.3110    0.2471    0.8487 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1592   -1.5000   -0.4053 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3229    1.4594    0.5658 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5176    1.8617   -1.7599 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9017    1.5500   -0.3581 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1949   -1.5871    0.1360 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2285   -0.8335   -1.5714 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5185   -0.2021    1.3347 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3112   -1.3313   -0.9006 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7850    0.8055    1.3862 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8122   -0.6916    1.3384 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5949    1.4890    0.9480 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2595    0.6677   -0.5557 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7060    1.6598   -0.5944 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1858   -2.0437   -0.3625 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  3
  2  3  1  0
  3  4  1  0
  3  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  2  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 13 15  1  0
  7  5  1  0
 12 10  1  0
  1 16  1  0
  1 17  1  0
  2 18  1  0
  3 19  1  1
  4 20  1  0
  5 21  1  6
  7 22  1  1
  8 23  1  0
  9 24  1  0
 10 25  1  6
 12 26  1  1
 13 27  1  1
 14 28  1  0
 14 29  1  0
 14 30  1  0
 15 31  1  0
M  END

HEADER    PROTEIN                                 24-JUN-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-JUN-21         0                                  
HETATM    1  C   UNK     0       5.807  -0.637   0.483  0.00  0.00           C+0
HETATM    2  C   UNK     0       4.609  -0.587  -0.060  0.00  0.00           C+0
HETATM    3  C   UNK     0       3.931   0.736  -0.171  0.00  0.00           C+0
HETATM    4  O   UNK     0       4.201   1.230  -1.438  0.00  0.00           O+0
HETATM    5  C   UNK     0       2.447   0.651   0.016  0.00  0.00           C+0
HETATM    6  O   UNK     0       1.933   0.180   1.217  0.00  0.00           O+0
HETATM    7  C   UNK     0       1.739  -0.604   0.028  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.358  -0.628  -0.514  0.00  0.00           C+0
HETATM    9  C   UNK     0      -0.661  -0.407   0.273  0.00  0.00           C+0
HETATM   10  C   UNK     0      -2.047  -0.438  -0.300  0.00  0.00           C+0
HETATM   11  O   UNK     0      -2.555   0.812  -0.700  0.00  0.00           O+0
HETATM   12  C   UNK     0      -3.090   0.201   0.497  0.00  0.00           C+0
HETATM   13  C   UNK     0      -4.529  -0.253   0.382  0.00  0.00           C+0
HETATM   14  C   UNK     0      -5.346   0.966   0.006  0.00  0.00           C+0
HETATM   15  O   UNK     0      -4.610  -1.187  -0.635  0.00  0.00           O+0
HETATM   16  H   UNK     0       6.353  -1.587   0.590  0.00  0.00           H+0
HETATM   17  H   UNK     0       6.311   0.247   0.849  0.00  0.00           H+0
HETATM   18  H   UNK     0       4.159  -1.500  -0.405  0.00  0.00           H+0
HETATM   19  H   UNK     0       4.323   1.459   0.566  0.00  0.00           H+0
HETATM   20  H   UNK     0       3.518   1.862  -1.760  0.00  0.00           H+0
HETATM   21  H   UNK     0       1.902   1.550  -0.358  0.00  0.00           H+0
HETATM   22  H   UNK     0       2.195  -1.587   0.136  0.00  0.00           H+0
HETATM   23  H   UNK     0       0.229  -0.834  -1.571  0.00  0.00           H+0
HETATM   24  H   UNK     0      -0.519  -0.202   1.335  0.00  0.00           H+0
HETATM   25  H   UNK     0      -2.311  -1.331  -0.901  0.00  0.00           H+0
HETATM   26  H   UNK     0      -2.785   0.806   1.386  0.00  0.00           H+0
HETATM   27  H   UNK     0      -4.812  -0.692   1.338  0.00  0.00           H+0
HETATM   28  H   UNK     0      -5.595   1.489   0.948  0.00  0.00           H+0
HETATM   29  H   UNK     0      -6.260   0.668  -0.556  0.00  0.00           H+0
HETATM   30  H   UNK     0      -4.706   1.660  -0.594  0.00  0.00           H+0
HETATM   31  H   UNK     0      -4.186  -2.044  -0.363  0.00  0.00           H+0
CONECT    1    2   16   17                                                  
CONECT    2    1    3   18                                                  
CONECT    3    2    4    5   19                                             
CONECT    4    3   20                                                       
CONECT    5    3    6    7   21                                             
CONECT    6    5    7                                                       
CONECT    7    6    8    5   22                                             
CONECT    8    7    9   23                                                  
CONECT    9    8   10   24                                                  
CONECT   10    9   11   12   25                                             
CONECT   11   10   12                                                       
CONECT   12   11   13   10   26                                             
CONECT   13   12   14   15   27                                             
CONECT   14   13   28   29   30                                             
CONECT   15   13   31                                                       
CONECT   16    1                                                            
CONECT   17    1                                                            
CONECT   18    2                                                            
CONECT   19    3                                                            
CONECT   20    4                                                            
CONECT   21    5                                                            
CONECT   22    7                                                            
CONECT   23    8                                                            
CONECT   24    9                                                            
CONECT   25   10                                                            
CONECT   26   12                                                            
CONECT   27   13                                                            
CONECT   28   14                                                            
CONECT   29   14                                                            
CONECT   30   14                                                            
CONECT   31   15                                                            
MASTER        0    0    0    0    0    0    0    0   31    0   64    0
END

RDKit          3D

31 32  0  0  0  0  0  0  0  0999 V2000
    5.8068   -0.6368    0.4829 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6085   -0.5868   -0.0603 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9310    0.7357   -0.1711 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.2008    1.2302   -1.4380 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4475    0.6507    0.0157 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.9327    0.1796    1.2172 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7389   -0.6037    0.0279 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.3580   -0.6284   -0.5144 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6613   -0.4073    0.2731 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0473   -0.4379   -0.2998 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.5551    0.8122   -0.6998 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0897    0.2014    0.4965 C   0  0  1  0  0  0  0  0  0  0  0  0
   -4.5295   -0.2526    0.3817 C   0  0  1  0  0  0  0  0  0  0  0  0
   -5.3463    0.9664    0.0055 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6104   -1.1870   -0.6354 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.3528   -1.5866    0.5898 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.3110    0.2471    0.8487 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1592   -1.5000   -0.4053 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3229    1.4594    0.5658 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5176    1.8617   -1.7599 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9017    1.5500   -0.3581 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1949   -1.5871    0.1360 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2285   -0.8335   -1.5714 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5185   -0.2021    1.3347 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3112   -1.3313   -0.9006 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7850    0.8055    1.3862 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8122   -0.6916    1.3384 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5949    1.4890    0.9480 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2595    0.6677   -0.5557 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7060    1.6598   -0.5944 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1858   -2.0437   -0.3625 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  3
  2  3  1  0
  3  4  1  0
  3  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  2  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 13 15  1  0
  7  5  1  0
 12 10  1  0
  1 16  1  0
  1 17  1  0
  2 18  1  0
  3 19  1  1
  4 20  1  0
  5 21  1  6
  7 22  1  1
  8 23  1  0
  9 24  1  0
 10 25  1  6
 12 26  1  1
 13 27  1  1
 14 28  1  0
 14 29  1  0
 14 30  1  0
 15 31  1  0
M  END

View in JSmol View NMR Assignments

Synonyms

Value	Source
(-)-Depudecin	ChEBI
4,5:8,9-Dianhydro-1,2,6,7,11-pentadeoxy-D-threo-D-ido-undeca-1,6-dienitol	ChEBI

Chemical Formula

C₁₁H₁₆O₄

Average Mass

212.2450 Da

Monoisotopic Mass

212.10486 Da

IUPAC Name

(1R)-1-[(2S,3S)-3-[(E)-2-[(2S,3S)-3-[(1R)-1-hydroxyethyl]oxiran-2-yl]ethenyl]oxiran-2-yl]prop-2-en-1-ol

Traditional Name

depudecin

CAS Registry Number

Not Available

SMILES

C[C@@H](O)[C@@H]1O[C@H]1\C=C\[C@@H]1O[C@H]1[C@H](O)C=C

InChI Identifier

InChI=1S/C11H16O4/c1-3-7(13)11-9(15-11)5-4-8-10(14-8)6(2)12/h3-13H,1H2,2H3/b5-4+/t6-,7-,8+,9+,10+,11+/m1/s1

InChI Key

DLVJMFOLJOOWFS-INMLLLKOSA-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, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, 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
Alternaria brassicicola	NPAtlas	1500354

Species Where Detected

Species Name	Source	Reference
Alternaria brassicicola RF-328	KNApSAcK Database	22123792

Chemical Taxonomy

Classification

Not classified

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	-0.27	ALOGPS
logP	0.33	ChemAxon
logS	-0.84	ALOGPS
pKa (Strongest Acidic)	13.67	ChemAxon
pKa (Strongest Basic)	-3.1	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	65.52 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	54.95 m³·mol⁻¹	ChemAxon
Polarizability	22.63 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

NPAtlas ID

NPA001465

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

C00017282

Chemspider ID

21169370

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

16219259

PDB ID

Not Available

ChEBI ID

64143

Good Scents ID

Not Available

References

General References

Matsumoto M, Matsutani S, Sugita K, Yoshida H, Hayashi F, Terui Y, Nakai H, Uotani N, Kawamura Y, Matsumoto K, et al.: Depudecin: a novel compound inducing the flat phenotype of NIH3T3 cells doubly transformed by ras- and src-oncogene, produced by Alternaria brassicicola. J Antibiot (Tokyo). 1992 Jun;45(6):879-85. doi: 10.7164/antibiotics.45.879. [PubMed:1500354 ]
Tanaka M, Fujimori T, Nabeta K: Biosynthesis of depudecin, a metabolite of Nimbya scirpicola. Biosci Biotechnol Biochem. 2000 Feb;64(2):244-7. doi: 10.1271/bbb.64.244. [PubMed:10737176 ]
Jung M: Inhibitors of histone deacetylase as new anticancer agents. Curr Med Chem. 2001 Oct;8(12):1505-11. doi: 10.2174/0929867013372058. [PubMed:11562279 ]
Kwon HJ, Kim JH, Kim M, Lee JK, Hwang WS, Kim DY: Anti-parasitic activity of depudecin on Neospora caninum via the inhibition of histone deacetylase. Vet Parasitol. 2003 Mar 25;112(4):269-76. doi: 10.1016/s0304-4017(03)00035-9. [PubMed:12623206 ]
Sugita K, Yoshida H, Matsumoto M, Matsutani S: A novel compound, depudecin, induces production of transformation to the flat phenotype of NIH3T3 cells transformed by ras-oncogene. Biochem Biophys Res Commun. 1992 Jan 15;182(1):379-87. doi: 10.1016/s0006-291x(05)80156-1. [PubMed:1731795 ]

Showing NP-Card for Depudecin (NP0005176)

MOL for NP0005176 (Depudecin)

3D MOL for NP0005176 (Depudecin)

3D SDF for NP0005176 (Depudecin)

3D-SDF for NP0005176 (Depudecin)

PDB for NP0005176 (Depudecin)

3D PDB for NP0005176 (Depudecin)

SMILES for NP0005176 (Depudecin)

INCHI for NP0005176 (Depudecin)

Structure for NP0005176 (Depudecin)

3D Structure for NP0005176 (Depudecin)