NP-MRD: Showing NP-Card for ( Z)-6-benzylidene-3-hydroxymethyl-1,4-dimethyl-3-methylsulfanylpiperazine-2,5-dione (NP0007503)

Jump To Section:

Identification Spectra BioTaxonomy ChemoTaxonomy Physical properties Links References XML

Record Information

Version

1.0

Created at

2020-12-09 04:22:02 UTC

Updated at

2021-07-15 16:57:46 UTC

NP-MRD ID

NP0007503

Secondary Accession Numbers

None

Natural Product Identification

Common Name

( Z)-6-benzylidene-3-hydroxymethyl-1,4-dimethyl-3-methylsulfanylpiperazine-2,5-dione

Provided By

NPAtlas

Description

( Z)-6-benzylidene-3-hydroxymethyl-1,4-dimethyl-3-methylsulfanylpiperazine-2,5-dione is found in Unknown sp. strain CRIF2. It was first documented in 2008 (PMID: 18203053). Based on a literature review very few articles have been published on ( z)-6-benzylidene-3-hydroxymethyl-1,4-dimethyl-3-methylsulfanylpiperazine-2,5-dione.

Structure

MOL 3D MOL SDF 3D SDF PDB SMILES InChI


  Mrv1652306242118403D          

 39 40  0  0  0  0            999 V2000
    4.2354   -1.5365   -0.4037 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7578   -1.3731    0.6122 S   0  0  0  0  0  0  0  0  0  0  0  0
    2.1852    0.3571    0.6077 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.2297    1.1814    1.3061 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.3063    0.7472    2.6301 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9020    0.4959    1.3259 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9206    0.9300    2.5005 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3884    0.1603    0.7579 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5023   -0.1603    1.5930 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4315    0.1306   -0.6464 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5576   -0.0923   -1.2755 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8569   -0.3185   -0.7394 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4687   -1.5267   -0.9539 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7689   -1.7195   -0.5553 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4985   -0.7301    0.0634 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9023    0.4908    0.2882 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5778    0.6596   -0.1278 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8111    0.4299   -1.4082 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7924    0.4074   -2.6663 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0411    0.7460   -0.7857 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.1242    1.4287   -1.4706 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0291   -1.3079   -1.4861 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6084   -2.5907   -0.4210 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0295   -0.8329   -0.0919 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2358    0.9582    0.8516 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0164    2.2522    1.3266 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4172   -0.2218    2.7183 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0630   -1.0635    1.3798 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0281    0.6961    2.0576 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9796   -0.5465    2.5686 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4377   -0.0990   -2.4025 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9340   -2.3319   -1.4352 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2899   -2.6714   -0.7107 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5389   -0.9012    0.3761 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4370    1.3040    0.7732 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1654    1.6609    0.0828 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9887    1.4214   -2.5548 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0781    2.4958   -1.1052 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1177    1.0705   -1.2152 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  3  2  1  6  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  3  6  1  0  0  0  0
  6  7  2  0  0  0  0
  6  8  1  0  0  0  0
  8  9  1  0  0  0  0
  8 10  1  0  0  0  0
 10 11  2  0  0  0  0
 11 12  1  0  0  0  0
 12 13  2  0  0  0  0
 13 14  1  0  0  0  0
 14 15  2  0  0  0  0
 15 16  1  0  0  0  0
 16 17  2  0  0  0  0
 10 18  1  0  0  0  0
 18 19  2  0  0  0  0
 18 20  1  0  0  0  0
 20 21  1  0  0  0  0
 20  3  1  0  0  0  0
 17 12  1  0  0  0  0
  1 22  1  0  0  0  0
  1 23  1  0  0  0  0
  1 24  1  0  0  0  0
  4 25  1  0  0  0  0
  4 26  1  0  0  0  0
  5 27  1  0  0  0  0
  9 28  1  0  0  0  0
  9 29  1  0  0  0  0
  9 30  1  0  0  0  0
 11 31  1  0  0  0  0
 13 32  1  0  0  0  0
 14 33  1  0  0  0  0
 15 34  1  0  0  0  0
 16 35  1  0  0  0  0
 17 36  1  0  0  0  0
 21 37  1  0  0  0  0
 21 38  1  0  0  0  0
 21 39  1  0  0  0  0
M  END

     RDKit          3D

 39 40  0  0  0  0  0  0  0  0999 V2000
    4.2354   -1.5365   -0.4037 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7578   -1.3731    0.6122 S   0  0  0  0  0  0  0  0  0  0  0  0
    2.1852    0.3571    0.6077 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.2297    1.1814    1.3061 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3063    0.7472    2.6301 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9020    0.4959    1.3259 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9206    0.9300    2.5005 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3884    0.1603    0.7579 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5023   -0.1603    1.5930 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4315    0.1306   -0.6464 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5576   -0.0923   -1.2755 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8569   -0.3185   -0.7394 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4687   -1.5267   -0.9539 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7689   -1.7195   -0.5553 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4985   -0.7301    0.0634 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9023    0.4908    0.2882 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5778    0.6596   -0.1278 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8111    0.4299   -1.4082 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7924    0.4074   -2.6663 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0411    0.7460   -0.7857 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.1242    1.4287   -1.4706 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0291   -1.3079   -1.4861 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6084   -2.5907   -0.4210 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0295   -0.8329   -0.0919 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2358    0.9582    0.8516 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0164    2.2522    1.3266 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4172   -0.2218    2.7183 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0630   -1.0635    1.3798 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0281    0.6961    2.0576 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9796   -0.5465    2.5686 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4377   -0.0990   -2.4025 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9340   -2.3319   -1.4352 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2899   -2.6714   -0.7107 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5389   -0.9012    0.3761 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4370    1.3040    0.7732 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1654    1.6609    0.0828 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9887    1.4214   -2.5548 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0781    2.4958   -1.1052 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1177    1.0705   -1.2152 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  3  2  1  6
  3  4  1  0
  4  5  1  0
  3  6  1  0
  6  7  2  0
  6  8  1  0
  8  9  1  0
  8 10  1  0
 10 11  2  0
 11 12  1  0
 12 13  2  0
 13 14  1  0
 14 15  2  0
 15 16  1  0
 16 17  2  0
 10 18  1  0
 18 19  2  0
 18 20  1  0
 20 21  1  0
 20  3  1  0
 17 12  1  0
  1 22  1  0
  1 23  1  0
  1 24  1  0
  4 25  1  0
  4 26  1  0
  5 27  1  0
  9 28  1  0
  9 29  1  0
  9 30  1  0
 11 31  1  0
 13 32  1  0
 14 33  1  0
 15 34  1  0
 16 35  1  0
 17 36  1  0
 21 37  1  0
 21 38  1  0
 21 39  1  0
M  END


  Mrv1652306242118403D          

 39 40  0  0  0  0            999 V2000
    4.2354   -1.5365   -0.4037 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7578   -1.3731    0.6122 S   0  0  0  0  0  0  0  0  0  0  0  0
    2.1852    0.3571    0.6077 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.2297    1.1814    1.3061 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.3063    0.7472    2.6301 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9020    0.4959    1.3259 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9206    0.9300    2.5005 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3884    0.1603    0.7579 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5023   -0.1603    1.5930 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4315    0.1306   -0.6464 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5576   -0.0923   -1.2755 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8569   -0.3185   -0.7394 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4687   -1.5267   -0.9539 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7689   -1.7195   -0.5553 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4985   -0.7301    0.0634 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9023    0.4908    0.2882 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5778    0.6596   -0.1278 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8111    0.4299   -1.4082 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7924    0.4074   -2.6663 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0411    0.7460   -0.7857 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.1242    1.4287   -1.4706 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0291   -1.3079   -1.4861 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6084   -2.5907   -0.4210 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0295   -0.8329   -0.0919 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2358    0.9582    0.8516 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0164    2.2522    1.3266 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4172   -0.2218    2.7183 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0630   -1.0635    1.3798 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0281    0.6961    2.0576 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9796   -0.5465    2.5686 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4377   -0.0990   -2.4025 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9340   -2.3319   -1.4352 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2899   -2.6714   -0.7107 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5389   -0.9012    0.3761 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4370    1.3040    0.7732 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1654    1.6609    0.0828 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9887    1.4214   -2.5548 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0781    2.4958   -1.1052 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1177    1.0705   -1.2152 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  3  2  1  6  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  3  6  1  0  0  0  0
  6  7  2  0  0  0  0
  6  8  1  0  0  0  0
  8  9  1  0  0  0  0
  8 10  1  0  0  0  0
 10 11  2  0  0  0  0
 11 12  1  0  0  0  0
 12 13  2  0  0  0  0
 13 14  1  0  0  0  0
 14 15  2  0  0  0  0
 15 16  1  0  0  0  0
 16 17  2  0  0  0  0
 10 18  1  0  0  0  0
 18 19  2  0  0  0  0
 18 20  1  0  0  0  0
 20 21  1  0  0  0  0
 20  3  1  0  0  0  0
 17 12  1  0  0  0  0
  1 22  1  0  0  0  0
  1 23  1  0  0  0  0
  1 24  1  0  0  0  0
  4 25  1  0  0  0  0
  4 26  1  0  0  0  0
  5 27  1  0  0  0  0
  9 28  1  0  0  0  0
  9 29  1  0  0  0  0
  9 30  1  0  0  0  0
 11 31  1  0  0  0  0
 13 32  1  0  0  0  0
 14 33  1  0  0  0  0
 15 34  1  0  0  0  0
 16 35  1  0  0  0  0
 17 36  1  0  0  0  0
 21 37  1  0  0  0  0
 21 38  1  0  0  0  0
 21 39  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0007503

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H]OC([H])([H])[C@]1(SC([H])([H])[H])N(C(=O)\C(=C(/[H])C2=C([H])C([H])=C([H])C([H])=C2[H])N(C1=O)C([H])([H])[H])C([H])([H])[H]

> <INCHI_IDENTIFIER>
InChI=1S/C15H18N2O3S/c1-16-12(9-11-7-5-4-6-8-11)13(19)17(2)15(10-18,21-3)14(16)20/h4-9,18H,10H2,1-3H3/b12-9-/t15-/m1/s1

> <INCHI_KEY>
HKUWFXOAQGVJHR-HMVFGEFZSA-N

> <FORMULA>
C15H18N2O3S

> <MOLECULAR_WEIGHT>
306.38

> <EXACT_MASS>
306.103813622

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
39

> <JCHEM_AVERAGE_POLARIZABILITY>
31.912298319431933

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(3R,6Z)-3-(hydroxymethyl)-1,4-dimethyl-3-(methylsulfanyl)-6-(phenylmethylidene)piperazine-2,5-dione

> <ALOGPS_LOGP>
1.00

> <JCHEM_LOGP>
1.2796910056666673

> <ALOGPS_LOGS>
-2.82

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
14.18693240449523

> <JCHEM_PKA_STRONGEST_BASIC>
-0.8453755131224735

> <JCHEM_POLAR_SURFACE_AREA>
60.85

> <JCHEM_REFRACTIVITY>
84.43980000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.67e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(3R,6Z)-3-(hydroxymethyl)-1,4-dimethyl-3-(methylsulfanyl)-6-(phenylmethylidene)piperazine-2,5-dione

> <JCHEM_VEBER_RULE>
0

$$$$

     RDKit          3D

 39 40  0  0  0  0  0  0  0  0999 V2000
    4.2354   -1.5365   -0.4037 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7578   -1.3731    0.6122 S   0  0  0  0  0  0  0  0  0  0  0  0
    2.1852    0.3571    0.6077 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.2297    1.1814    1.3061 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3063    0.7472    2.6301 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9020    0.4959    1.3259 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9206    0.9300    2.5005 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3884    0.1603    0.7579 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5023   -0.1603    1.5930 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4315    0.1306   -0.6464 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5576   -0.0923   -1.2755 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8569   -0.3185   -0.7394 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4687   -1.5267   -0.9539 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7689   -1.7195   -0.5553 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4985   -0.7301    0.0634 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9023    0.4908    0.2882 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5778    0.6596   -0.1278 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8111    0.4299   -1.4082 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7924    0.4074   -2.6663 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0411    0.7460   -0.7857 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.1242    1.4287   -1.4706 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0291   -1.3079   -1.4861 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6084   -2.5907   -0.4210 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0295   -0.8329   -0.0919 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2358    0.9582    0.8516 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0164    2.2522    1.3266 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4172   -0.2218    2.7183 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0630   -1.0635    1.3798 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0281    0.6961    2.0576 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9796   -0.5465    2.5686 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4377   -0.0990   -2.4025 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9340   -2.3319   -1.4352 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2899   -2.6714   -0.7107 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5389   -0.9012    0.3761 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4370    1.3040    0.7732 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1654    1.6609    0.0828 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9887    1.4214   -2.5548 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0781    2.4958   -1.1052 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1177    1.0705   -1.2152 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  3  2  1  6
  3  4  1  0
  4  5  1  0
  3  6  1  0
  6  7  2  0
  6  8  1  0
  8  9  1  0
  8 10  1  0
 10 11  2  0
 11 12  1  0
 12 13  2  0
 13 14  1  0
 14 15  2  0
 15 16  1  0
 16 17  2  0
 10 18  1  0
 18 19  2  0
 18 20  1  0
 20 21  1  0
 20  3  1  0
 17 12  1  0
  1 22  1  0
  1 23  1  0
  1 24  1  0
  4 25  1  0
  4 26  1  0
  5 27  1  0
  9 28  1  0
  9 29  1  0
  9 30  1  0
 11 31  1  0
 13 32  1  0
 14 33  1  0
 15 34  1  0
 16 35  1  0
 17 36  1  0
 21 37  1  0
 21 38  1  0
 21 39  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       4.235  -1.537  -0.404  0.00  0.00           C+0
HETATM    2  S   UNK     0       2.758  -1.373   0.612  0.00  0.00           S+0
HETATM    3  C   UNK     0       2.185   0.357   0.608  0.00  0.00           C+0
HETATM    4  C   UNK     0       3.230   1.181   1.306  0.00  0.00           C+0
HETATM    5  O   UNK     0       3.306   0.747   2.630  0.00  0.00           O+0
HETATM    6  C   UNK     0       0.902   0.496   1.326  0.00  0.00           C+0
HETATM    7  O   UNK     0       0.921   0.930   2.501  0.00  0.00           O+0
HETATM    8  N   UNK     0      -0.388   0.160   0.758  0.00  0.00           N+0
HETATM    9  C   UNK     0      -1.502  -0.160   1.593  0.00  0.00           C+0
HETATM   10  C   UNK     0      -0.432   0.131  -0.646  0.00  0.00           C+0
HETATM   11  C   UNK     0      -1.558  -0.092  -1.276  0.00  0.00           C+0
HETATM   12  C   UNK     0      -2.857  -0.319  -0.739  0.00  0.00           C+0
HETATM   13  C   UNK     0      -3.469  -1.527  -0.954  0.00  0.00           C+0
HETATM   14  C   UNK     0      -4.769  -1.720  -0.555  0.00  0.00           C+0
HETATM   15  C   UNK     0      -5.498  -0.730   0.063  0.00  0.00           C+0
HETATM   16  C   UNK     0      -4.902   0.491   0.288  0.00  0.00           C+0
HETATM   17  C   UNK     0      -3.578   0.660  -0.128  0.00  0.00           C+0
HETATM   18  C   UNK     0       0.811   0.430  -1.408  0.00  0.00           C+0
HETATM   19  O   UNK     0       0.792   0.407  -2.666  0.00  0.00           O+0
HETATM   20  N   UNK     0       2.041   0.746  -0.786  0.00  0.00           N+0
HETATM   21  C   UNK     0       3.124   1.429  -1.471  0.00  0.00           C+0
HETATM   22  H   UNK     0       4.029  -1.308  -1.486  0.00  0.00           H+0
HETATM   23  H   UNK     0       4.608  -2.591  -0.421  0.00  0.00           H+0
HETATM   24  H   UNK     0       5.029  -0.833  -0.092  0.00  0.00           H+0
HETATM   25  H   UNK     0       4.236   0.958   0.852  0.00  0.00           H+0
HETATM   26  H   UNK     0       3.016   2.252   1.327  0.00  0.00           H+0
HETATM   27  H   UNK     0       3.417  -0.222   2.718  0.00  0.00           H+0
HETATM   28  H   UNK     0      -2.063  -1.063   1.380  0.00  0.00           H+0
HETATM   29  H   UNK     0      -2.028   0.696   2.058  0.00  0.00           H+0
HETATM   30  H   UNK     0      -0.980  -0.547   2.569  0.00  0.00           H+0
HETATM   31  H   UNK     0      -1.438  -0.099  -2.402  0.00  0.00           H+0
HETATM   32  H   UNK     0      -2.934  -2.332  -1.435  0.00  0.00           H+0
HETATM   33  H   UNK     0      -5.290  -2.671  -0.711  0.00  0.00           H+0
HETATM   34  H   UNK     0      -6.539  -0.901   0.376  0.00  0.00           H+0
HETATM   35  H   UNK     0      -5.437   1.304   0.773  0.00  0.00           H+0
HETATM   36  H   UNK     0      -3.165   1.661   0.083  0.00  0.00           H+0
HETATM   37  H   UNK     0       2.989   1.421  -2.555  0.00  0.00           H+0
HETATM   38  H   UNK     0       3.078   2.496  -1.105  0.00  0.00           H+0
HETATM   39  H   UNK     0       4.118   1.071  -1.215  0.00  0.00           H+0
CONECT    1    2   22   23   24                                             
CONECT    2    1    3                                                       
CONECT    3    2    4    6   20                                             
CONECT    4    3    5   25   26                                             
CONECT    5    4   27                                                       
CONECT    6    3    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    9   10                                                  
CONECT    9    8   28   29   30                                             
CONECT   10    8   11   18                                                  
CONECT   11   10   12   31                                                  
CONECT   12   11   13   17                                                  
CONECT   13   12   14   32                                                  
CONECT   14   13   15   33                                                  
CONECT   15   14   16   34                                                  
CONECT   16   15   17   35                                                  
CONECT   17   16   12   36                                                  
CONECT   18   10   19   20                                                  
CONECT   19   18                                                            
CONECT   20   18   21    3                                                  
CONECT   21   20   37   38   39                                             
CONECT   22    1                                                            
CONECT   23    1                                                            
CONECT   24    1                                                            
CONECT   25    4                                                            
CONECT   26    4                                                            
CONECT   27    5                                                            
CONECT   28    9                                                            
CONECT   29    9                                                            
CONECT   30    9                                                            
CONECT   31   11                                                            
CONECT   32   13                                                            
CONECT   33   14                                                            
CONECT   34   15                                                            
CONECT   35   16                                                            
CONECT   36   17                                                            
CONECT   37   21                                                            
CONECT   38   21                                                            
CONECT   39   21                                                            
MASTER        0    0    0    0    0    0    0    0   39    0   80    0
END

RDKit          3D

39 40  0  0  0  0  0  0  0  0999 V2000
    4.2354   -1.5365   -0.4037 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7578   -1.3731    0.6122 S   0  0  0  0  0  0  0  0  0  0  0  0
    2.1852    0.3571    0.6077 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.2297    1.1814    1.3061 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3063    0.7472    2.6301 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9020    0.4959    1.3259 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9206    0.9300    2.5005 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3884    0.1603    0.7579 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5023   -0.1603    1.5930 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4315    0.1306   -0.6464 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5576   -0.0923   -1.2755 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8569   -0.3185   -0.7394 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4687   -1.5267   -0.9539 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7689   -1.7195   -0.5553 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4985   -0.7301    0.0634 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9023    0.4908    0.2882 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5778    0.6596   -0.1278 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8111    0.4299   -1.4082 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7924    0.4074   -2.6663 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0411    0.7460   -0.7857 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.1242    1.4287   -1.4706 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0291   -1.3079   -1.4861 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6084   -2.5907   -0.4210 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0295   -0.8329   -0.0919 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2358    0.9582    0.8516 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0164    2.2522    1.3266 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4172   -0.2218    2.7183 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0630   -1.0635    1.3798 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0281    0.6961    2.0576 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9796   -0.5465    2.5686 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4377   -0.0990   -2.4025 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9340   -2.3319   -1.4352 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2899   -2.6714   -0.7107 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5389   -0.9012    0.3761 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4370    1.3040    0.7732 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1654    1.6609    0.0828 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9887    1.4214   -2.5548 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0781    2.4958   -1.1052 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1177    1.0705   -1.2152 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  3  2  1  6
  3  4  1  0
  4  5  1  0
  3  6  1  0
  6  7  2  0
  6  8  1  0
  8  9  1  0
  8 10  1  0
 10 11  2  0
 11 12  1  0
 12 13  2  0
 13 14  1  0
 14 15  2  0
 15 16  1  0
 16 17  2  0
 10 18  1  0
 18 19  2  0
 18 20  1  0
 20 21  1  0
 20  3  1  0
 17 12  1  0
  1 22  1  0
  1 23  1  0
  1 24  1  0
  4 25  1  0
  4 26  1  0
  5 27  1  0
  9 28  1  0
  9 29  1  0
  9 30  1  0
 11 31  1  0
 13 32  1  0
 14 33  1  0
 15 34  1  0
 16 35  1  0
 17 36  1  0
 21 37  1  0
 21 38  1  0
 21 39  1  0
M  END

View in JSmol View NMR Assignments

Synonyms

Value	Source
( Z)-6-Benzylidene-3-hydroxymethyl-1,4-dimethyl-3-methylsulphanylpiperazine-2,5-dione	Generator
(3R,6Z)-3-(Hydroxymethyl)-1,4-dimethyl-3-(methylsulphanyl)-6-(phenylmethylidene)piperazine-2,5-dione	Generator

Chemical Formula

C₁₅H₁₈N₂O₃S

Average Mass

306.3800 Da

Monoisotopic Mass

306.10381 Da

IUPAC Name

(3R,6Z)-3-(hydroxymethyl)-1,4-dimethyl-3-(methylsulfanyl)-6-(phenylmethylidene)piperazine-2,5-dione

Traditional Name

(3R,6Z)-3-(hydroxymethyl)-1,4-dimethyl-3-(methylsulfanyl)-6-(phenylmethylidene)piperazine-2,5-dione

CAS Registry Number

Not Available

SMILES

CS[C@@]1(CO)N(C)C(=O)\C(=C\C2=CC=CC=C2)N(C)C1=O

InChI Identifier

InChI=1S/C15H18N2O3S/c1-16-12(9-11-7-5-4-6-8-11)13(19)17(2)15(10-18,21-3)14(16)20/h4-9,18H,10H2,1-3H3/b12-9-/t15-/m1/s1

InChI Key

HKUWFXOAQGVJHR-HMVFGEFZSA-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
Unknown sp. strain CRIF2	NPAtlas	18203053

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	1	ALOGPS
logP	1.28	ChemAxon
logS	-2.8	ALOGPS
pKa (Strongest Acidic)	14.19	ChemAxon
pKa (Strongest Basic)	-0.85	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	60.85 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	84.44 m³·mol⁻¹	ChemAxon
Polarizability	31.91 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

NPA007042

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

27023190

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

139585079

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Prachyawarakorn V, Mahidol C, Sureram S, Sangpetsiripan S, Wiyakrutta S, Ruchirawat S, Kittakoop P: Diketopiperazines and phthalides from a marine derived fungus of the order pleosporales. Planta Med. 2008 Jan;74(1):69-72. doi: 10.1055/s-2007-993783. Epub 2008 Jan 17. [PubMed:18203053 ]

Showing NP-Card for ( Z)-6-benzylidene-3-hydroxymethyl-1,4-dimethyl-3-methylsulfanylpiperazine-2,5-dione (NP0007503)

MOL for NP0007503 (( Z)-6-benzylidene-3-hydroxymethyl-1,4-dimethyl-3-methylsulfanylpiperazine-2,5-dione)

3D MOL for NP0007503 (( Z)-6-benzylidene-3-hydroxymethyl-1,4-dimethyl-3-methylsulfanylpiperazine-2,5-dione)

3D SDF for NP0007503 (( Z)-6-benzylidene-3-hydroxymethyl-1,4-dimethyl-3-methylsulfanylpiperazine-2,5-dione)

3D-SDF for NP0007503 (( Z)-6-benzylidene-3-hydroxymethyl-1,4-dimethyl-3-methylsulfanylpiperazine-2,5-dione)

PDB for NP0007503 (( Z)-6-benzylidene-3-hydroxymethyl-1,4-dimethyl-3-methylsulfanylpiperazine-2,5-dione)

3D PDB for NP0007503 (( Z)-6-benzylidene-3-hydroxymethyl-1,4-dimethyl-3-methylsulfanylpiperazine-2,5-dione)

SMILES for NP0007503 (( Z)-6-benzylidene-3-hydroxymethyl-1,4-dimethyl-3-methylsulfanylpiperazine-2,5-dione)

INCHI for NP0007503 (( Z)-6-benzylidene-3-hydroxymethyl-1,4-dimethyl-3-methylsulfanylpiperazine-2,5-dione)

Structure for NP0007503 (( Z)-6-benzylidene-3-hydroxymethyl-1,4-dimethyl-3-methylsulfanylpiperazine-2,5-dione)

3D Structure for NP0007503 (( Z)-6-benzylidene-3-hydroxymethyl-1,4-dimethyl-3-methylsulfanylpiperazine-2,5-dione)