NP-MRD: Showing NP-Card for (3s,6s)-3-benzyl-1,4-dimethyl-6-[(4-nitro-1h-indol-3-yl)methyl]piperazine-2,5-dione (NP0319560)

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Record Information

Version

2.0

Created at

2022-09-11 20:38:57 UTC

Updated at

2022-09-11 20:38:57 UTC

NP-MRD ID

NP0319560

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(3s,6s)-3-benzyl-1,4-dimethyl-6-[(4-nitro-1h-indol-3-yl)methyl]piperazine-2,5-dione

Description

Thaxtomin D belongs to the class of organic compounds known as alpha amino acids and derivatives. These are amino acids in which the amino group is attached to the carbon atom immediately adjacent to the carboxylate group (alpha carbon), or a derivative thereof. (3s,6s)-3-benzyl-1,4-dimethyl-6-[(4-nitro-1h-indol-3-yl)methyl]piperazine-2,5-dione was first documented in 2006 (PMID: 16637698). Based on a literature review a small amount of articles have been published on Thaxtomin D (PMID: 33861573) (PMID: 30516965).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309112222382D          

 30 33  0  0  1  0            999 V2000
   -1.2400   -4.0623    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9851   -3.2777    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1781   -3.1062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3739   -3.7192    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0768   -2.3215    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.8838   -2.1500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387   -1.3654    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6538   -0.6979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387   -0.0305    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233   -0.2854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    0.1271    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523   -0.2854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523   -1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378   -1.5229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378   -2.3479    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
    1.9233   -2.7604    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523   -2.7604    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    1.9233   -1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4752   -1.7084    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2203   -0.9238    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2822   -1.8800    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8342   -1.2669    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5371   -2.6646    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.3441   -2.8361    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5990   -3.6207    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0470   -4.2338    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3020   -5.0184    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1089   -5.1900    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6610   -4.5769    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4060   -3.7923    0.0000 C   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  2  0  0  0  0
  3  5  1  0  0  0  0
  5  6  1  1  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  8  9  1  0  0  0  0
  9 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  1  0  0  0  0
 15 16  2  0  0  0  0
 15 17  1  0  0  0  0
 14 18  2  0  0  0  0
  7 18  1  0  0  0  0
 10 18  1  0  0  0  0
  5 19  1  0  0  0  0
 19 20  1  0  0  0  0
 19 21  1  0  0  0  0
 21 22  2  0  0  0  0
 21 23  1  0  0  0  0
  2 23  1  0  0  0  0
 23 24  1  1  0  0  0
 24 25  1  0  0  0  0
 25 26  2  0  0  0  0
 26 27  1  0  0  0  0
 27 28  2  0  0  0  0
 28 29  1  0  0  0  0
 29 30  2  0  0  0  0
 25 30  1  0  0  0  0
M  CHG  2  15   1  17  -1
M  END

     RDKit          3D

 52 55  0  0  0  0  0  0  0  0999 V2000
   -2.4469   -1.2907    2.3178 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6365   -0.6186    1.3234 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2923   -1.0777    1.1021 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3855   -1.5487    2.0184 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2381   -0.9605   -0.2650 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.6760   -1.4659   -0.2906 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1984   -1.5799   -1.6695 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4151   -2.0833   -2.7339 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0732   -1.8685   -3.8658 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.2443   -1.2538   -3.5844 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2500   -0.8254   -4.4162 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3707   -0.2112   -3.9098 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4954   -0.0257   -2.5676 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4784   -0.4596   -1.7042 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7366   -0.3066   -0.3306 N   0  0  0  0  0  4  0  0  0  0  0  0
    5.4111    0.7007    0.0658 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.3006   -1.1849    0.6048 O   0  0  0  0  0  1  0  0  0  0  0  0
    3.3517   -1.0639   -2.2013 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0059    0.3266   -0.8023 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.9962    1.1451   -1.5069 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3315    0.8340   -0.6265 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8365    1.6156   -1.4636 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1702    0.4578    0.5597 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.4023    1.7370    1.3154 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3412    1.6226    2.4439 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8972    1.4520    3.7385 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7888    1.3258    4.7882 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1403    1.3708    4.5323 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6084    1.5425    3.2330 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7006    1.6678    2.1985 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5191   -2.3881    2.0749 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0006   -1.2193    3.3109 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4841   -0.9220    2.3090 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3107   -1.7025   -0.9211 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7498   -2.3760    0.2785 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2187   -0.5955    0.1834 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4659   -2.5445   -2.5747 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6996   -2.1539   -4.8211 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1569   -0.9747   -5.4690 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.1463    0.1158   -4.5752 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.3585    0.4495   -2.1040 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9186    1.2630   -0.8818 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2138    0.7905   -2.5132 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5672    2.1868   -1.5455 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1482    0.1052    0.1456 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8194    2.5393    0.6487 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4239    2.1751    1.6752 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8255    1.4239    3.8797 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4130    1.1972    5.7718 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8510    1.2704    5.3361 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.6515    1.5843    2.9834 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0711    1.8022    1.1827 H   0  0  0  0  0  0  0  0  0  0  0  0
 20 19  1  0
 19  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  2  0
  8  9  1  0
  9 10  1  0
 10 11  2  0
 11 12  1  0
 12 13  2  0
 13 14  1  0
 14 18  2  0
 14 15  1  0
 15 17  1  0
 15 16  2  0
  5  3  1  0
  3  4  2  0
  3  2  1  0
  2  1  1  0
  2 23  1  0
 23 24  1  0
 24 25  1  0
 25 26  2  0
 26 27  1  0
 27 28  2  0
 28 29  1  0
 29 30  2  0
 23 21  1  0
 21 22  2  0
 21 19  1  0
 18  7  1  0
 30 25  1  0
 18 10  1  0
 20 42  1  0
 20 43  1  0
 20 44  1  0
  5 34  1  6
  6 35  1  0
  6 36  1  0
  8 37  1  0
  9 38  1  0
 11 39  1  0
 12 40  1  0
 13 41  1  0
  1 31  1  0
  1 32  1  0
  1 33  1  0
 23 45  1  6
 24 46  1  0
 24 47  1  0
 26 48  1  0
 27 49  1  0
 28 50  1  0
 29 51  1  0
 30 52  1  0
M  CHG  2  15   1  17  -1
M  END


  Mrv1652309112222382D          

 30 33  0  0  1  0            999 V2000
   -1.2400   -4.0623    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9851   -3.2777    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1781   -3.1062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3739   -3.7192    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0768   -2.3215    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.8838   -2.1500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387   -1.3654    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6538   -0.6979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387   -0.0305    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233   -0.2854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    0.1271    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523   -0.2854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523   -1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378   -1.5229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378   -2.3479    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
    1.9233   -2.7604    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523   -2.7604    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    1.9233   -1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4752   -1.7084    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2203   -0.9238    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2822   -1.8800    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8342   -1.2669    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5371   -2.6646    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.3441   -2.8361    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5990   -3.6207    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0470   -4.2338    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3020   -5.0184    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1089   -5.1900    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6610   -4.5769    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4060   -3.7923    0.0000 C   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  2  0  0  0  0
  3  5  1  0  0  0  0
  5  6  1  1  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  8  9  1  0  0  0  0
  9 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  1  0  0  0  0
 15 16  2  0  0  0  0
 15 17  1  0  0  0  0
 14 18  2  0  0  0  0
  7 18  1  0  0  0  0
 10 18  1  0  0  0  0
  5 19  1  0  0  0  0
 19 20  1  0  0  0  0
 19 21  1  0  0  0  0
 21 22  2  0  0  0  0
 21 23  1  0  0  0  0
  2 23  1  0  0  0  0
 23 24  1  1  0  0  0
 24 25  1  0  0  0  0
 25 26  2  0  0  0  0
 26 27  1  0  0  0  0
 27 28  2  0  0  0  0
 28 29  1  0  0  0  0
 29 30  2  0  0  0  0
 25 30  1  0  0  0  0
M  CHG  2  15   1  17  -1
M  END
> <DATABASE_ID>
NP0319560

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CN1[C@@H](CC2=CNC3=CC=CC(=C23)[N+]([O-])=O)C(=O)N(C)[C@@H](CC2=CC=CC=C2)C1=O

> <INCHI_IDENTIFIER>
InChI=1S/C22H22N4O4/c1-24-18(11-14-7-4-3-5-8-14)21(27)25(2)19(22(24)28)12-15-13-23-16-9-6-10-17(20(15)16)26(29)30/h3-10,13,18-19,23H,11-12H2,1-2H3/t18-,19-/m0/s1

> <INCHI_KEY>
GJJXGBLNXDIHIQ-OALUTQOASA-N

> <FORMULA>
C22H22N4O4

> <MOLECULAR_WEIGHT>
406.442

> <EXACT_MASS>
406.164105204

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
52

> <JCHEM_AVERAGE_POLARIZABILITY>
40.79014172167909

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(3S,6S)-3-benzyl-1,4-dimethyl-6-[(4-nitro-1H-indol-3-yl)methyl]piperazine-2,5-dione

> <JCHEM_LOGP>
2.725713054333334

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
18.608835294393696

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.968486018351197

> <JCHEM_PKA_STRONGEST_BASIC>
-4.087681286821983

> <JCHEM_POLAR_SURFACE_AREA>
99.54999999999998

> <JCHEM_REFRACTIVITY>
111.0332

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(3S,6S)-3-benzyl-1,4-dimethyl-6-[(4-nitro-1H-indol-3-yl)methyl]piperazine-2,5-dione

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 11-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   11-SEP-22         0                                  
HETATM    1  C   UNK     0      -2.315  -7.583   0.000  0.00  0.00           C+0
HETATM    2  N   UNK     0      -1.839  -6.118   0.000  0.00  0.00           N+0
HETATM    3  C   UNK     0      -0.333  -5.798   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       0.698  -6.943   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       0.143  -4.334   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.650  -4.013   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       2.126  -2.549   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       1.220  -1.303   0.000  0.00  0.00           C+0
HETATM    9  N   UNK     0       2.126  -0.057   0.000  0.00  0.00           N+0
HETATM   10  C   UNK     0       3.590  -0.533   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       4.924   0.237   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       6.258  -0.533   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       6.258  -2.073   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       4.924  -2.843   0.000  0.00  0.00           C+0
HETATM   15  N   UNK     0       4.924  -4.383   0.000  0.00  0.00           N+1
HETATM   16  O   UNK     0       3.590  -5.153   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0       6.258  -5.153   0.000  0.00  0.00           O-1
HETATM   18  C   UNK     0       3.590  -2.073   0.000  0.00  0.00           C+0
HETATM   19  N   UNK     0      -0.887  -3.189   0.000  0.00  0.00           N+0
HETATM   20  C   UNK     0      -0.411  -1.724   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      -2.393  -3.509   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0      -3.424  -2.365   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0      -2.869  -4.974   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      -4.376  -5.294   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      -4.852  -6.759   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      -3.821  -7.903   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      -4.297  -9.368   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      -5.803  -9.688   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      -6.834  -8.544   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      -6.358  -7.079   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3   23                                                  
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6   19                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8   18                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11   18                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15   18                                                  
CONECT   15   14   16   17                                                  
CONECT   16   15                                                            
CONECT   17   15                                                            
CONECT   18   14    7   10                                                  
CONECT   19    5   20   21                                                  
CONECT   20   19                                                            
CONECT   21   19   22   23                                                  
CONECT   22   21                                                            
CONECT   23   21    2   24                                                  
CONECT   24   23   25                                                       
CONECT   25   24   26   30                                                  
CONECT   26   25   27                                                       
CONECT   27   26   28                                                       
CONECT   28   27   29                                                       
CONECT   29   28   30                                                       
CONECT   30   29   25                                                       
MASTER        0    0    0    0    0    0    0    0   30    0   66    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₂H₂₂N₄O₄

Average Mass

406.4420 Da

Monoisotopic Mass

406.16411 Da

IUPAC Name

(3S,6S)-3-benzyl-1,4-dimethyl-6-[(4-nitro-1H-indol-3-yl)methyl]piperazine-2,5-dione

Traditional Name

(3S,6S)-3-benzyl-1,4-dimethyl-6-[(4-nitro-1H-indol-3-yl)methyl]piperazine-2,5-dione

CAS Registry Number

Not Available

SMILES

CN1[C@@H](CC2=CNC3=CC=CC(=C23)[N+]([O-])=O)C(=O)N(C)[C@@H](CC2=CC=CC=C2)C1=O

InChI Identifier

InChI=1S/C22H22N4O4/c1-24-18(11-14-7-4-3-5-8-14)21(27)25(2)19(22(24)28)12-15-13-23-16-9-6-10-17(20(15)16)26(29)30/h3-10,13,18-19,23H,11-12H2,1-2H3/t18-,19-/m0/s1

InChI Key

GJJXGBLNXDIHIQ-OALUTQOASA-N

Experimental Spectra

Not Available

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 25 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Not Available

Species

Species of Origin

Not Available

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as alpha amino acids and derivatives. These are amino acids in which the amino group is attached to the carbon atom immediately adjacent to the carboxylate group (alpha carbon), or a derivative thereof.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

Alpha amino acids and derivatives

Alternative Parents

Substituents

Alpha-amino acid or derivatives
3-alkylindole
Indole
Indole or derivatives
Nitroaromatic compound
Dioxopiperazine
2,5-dioxopiperazine
N-alkylpiperazine
N-methylpiperazine
Monocyclic benzene moiety
1,4-diazinane
Benzenoid
Piperazine
Substituted pyrrole
Heteroaromatic compound
Tertiary carboxylic acid amide
Pyrrole
Carboxamide group
Organic nitro compound
Lactam
C-nitro compound
Organoheterocyclic compound
Organic oxoazanium
Azacycle
Organic 1,3-dipolar compound
Propargyl-type 1,3-dipolar organic compound
Allyl-type 1,3-dipolar organic compound
Organic salt
Organooxygen compound
Organonitrogen compound
Carbonyl group
Organic oxygen compound
Hydrocarbon derivative
Organic oxide
Organic nitrogen compound
Organic zwitterion
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

Not Available

Physical Properties

State

Not Available

Experimental Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Predicted Properties

Property	Value	Source
logP	2.73	ChemAxon
pKa (Strongest Acidic)	12.97	ChemAxon
pKa (Strongest Basic)	-4.1	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	99.55 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	111.03 m³·mol⁻¹	ChemAxon
Polarizability	40.79 Å³	ChemAxon
Number of Rings	4	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

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

101712792

PDB ID

C8H

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Yuan C, Ouyang Q, Wang X, Li X, Tan H, Chen G: Interactive Regulation between Aliphatic Hydroxylation and Aromatic Hydroxylation of Thaxtomin D in TxtC: A Theoretical Investigation. Inorg Chem. 2021 May 3;60(9):6433-6445. doi: 10.1021/acs.inorgchem.1c00154. Epub 2021 Apr 16. [PubMed:33861573 ]
Hiltunen LH, Laakso I, Chobot V, Hakala KS, Weckman A, Valkonen JP: Influence of thaxtomins in different combinations and concentrations on growth of micropropagated potato shoot cultures. J Agric Food Chem. 2006 May 3;54(9):3372-9. doi: 10.1021/jf060270m. [PubMed:16637698 ]
Alkhalaf LM, Barry SM, Rea D, Gallo A, Griffiths D, Lewandowski JR, Fulop V, Challis GL: Binding of Distinct Substrate Conformations Enables Hydroxylation of Remote Sites in Thaxtomin D by Cytochrome P450 TxtC. J Am Chem Soc. 2019 Jan 9;141(1):216-222. doi: 10.1021/jacs.8b08864. Epub 2018 Dec 19. [PubMed:30516965 ]
LOTUS database [Link]

Showing NP-Card for (3s,6s)-3-benzyl-1,4-dimethyl-6-[(4-nitro-1h-indol-3-yl)methyl]piperazine-2,5-dione (NP0319560)

MOL for NP0319560 ((3s,6s)-3-benzyl-1,4-dimethyl-6-[(4-nitro-1h-indol-3-yl)methyl]piperazine-2,5-dione)

3D MOL for NP0319560 ((3s,6s)-3-benzyl-1,4-dimethyl-6-[(4-nitro-1h-indol-3-yl)methyl]piperazine-2,5-dione)

3D SDF for NP0319560 ((3s,6s)-3-benzyl-1,4-dimethyl-6-[(4-nitro-1h-indol-3-yl)methyl]piperazine-2,5-dione)

3D-SDF for NP0319560 ((3s,6s)-3-benzyl-1,4-dimethyl-6-[(4-nitro-1h-indol-3-yl)methyl]piperazine-2,5-dione)

PDB for NP0319560 ((3s,6s)-3-benzyl-1,4-dimethyl-6-[(4-nitro-1h-indol-3-yl)methyl]piperazine-2,5-dione)

3D PDB for NP0319560 ((3s,6s)-3-benzyl-1,4-dimethyl-6-[(4-nitro-1h-indol-3-yl)methyl]piperazine-2,5-dione)

SMILES for NP0319560 ((3s,6s)-3-benzyl-1,4-dimethyl-6-[(4-nitro-1h-indol-3-yl)methyl]piperazine-2,5-dione)

INCHI for NP0319560 ((3s,6s)-3-benzyl-1,4-dimethyl-6-[(4-nitro-1h-indol-3-yl)methyl]piperazine-2,5-dione)

Structure for NP0319560 ((3s,6s)-3-benzyl-1,4-dimethyl-6-[(4-nitro-1h-indol-3-yl)methyl]piperazine-2,5-dione)

3D Structure for NP0319560 ((3s,6s)-3-benzyl-1,4-dimethyl-6-[(4-nitro-1h-indol-3-yl)methyl]piperazine-2,5-dione)