NP-MRD: Showing NP-Card for Agrochelin (NP0003135)

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Record Information

Version

1.0

Created at

2020-12-09 00:13:02 UTC

Updated at

2021-07-15 16:45:36 UTC

NP-MRD ID

NP0003135

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Agrochelin

Provided By

NPAtlas

Description

Agrochelin 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. Agrochelin is found in Agrobacterium. It was first documented in 1999 (PMID: 10656570). Based on a literature review very few articles have been published on agrochelin (PMID: 31293678).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652306242117453D          

 65 67  0  0  0  0            999 V2000
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M  END

     RDKit          3D

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M  END


  Mrv1652306242117453D          

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   -0.4301   -0.7221   -0.0318 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.3355    0.4888   -0.1020 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.1602    0.7926    1.5024 S   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8499    0.3230    0.9266 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.5630   -0.1687   -0.4382 C   0  0  1  0  0  0  0  0  0  0  0  0
   -4.7589    0.0620   -1.3094 C   0  0  1  0  0  0  0  0  0  0  0  0
   -4.5962   -0.4876   -2.5853 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0689   -0.3948   -0.7541 C   0  0  2  0  0  0  0  0  0  0  0  0
   -6.0842   -1.8804   -0.4529 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0716   -0.2399   -1.9320 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.6351    0.4302    0.3213 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.9890    1.6109    0.1009 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7885   -0.0781    1.5933 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4019    0.3976   -0.9898 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5265    1.3748   -1.9965 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1903   -0.8379   -1.4213 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.5095    0.4119   -1.0935 S   0  0  0  0  0  0  0  0  0  0  0  0
    8.4650   -0.2699    0.9807 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.3036    0.1061   -0.5978 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.4016   -1.4861   -0.4045 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.2900    0.4652   -1.7287 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.0232    1.1500   -0.0858 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.1797   -1.5746   -1.1389 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.9081   -1.1005    0.5440 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9752   -0.9428   -0.9299 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8420    0.1630   -2.0252 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4599    1.6238   -0.7655 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1334    1.8521   -0.2828 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8297    1.6373    1.8132 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5243    1.1604    4.2172 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3771    0.1182    4.9085 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5854   -0.8601    3.0812 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0024   -1.6437    0.2196 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6964    1.3660   -0.3237 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1264   -0.5166    1.6006 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4395    1.2283    1.0272 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4121   -1.2899   -0.4197 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8829    1.1714   -1.4988 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5121   -1.4718   -2.5616 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2840   -2.1946    0.2201 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1017   -2.4045   -1.4291 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0523   -2.0879    0.0531 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1570    0.8581   -2.0633 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.6848   -0.7206   -2.8366 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.0660   -0.6076   -1.6257 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.6940   -0.2565    2.0121 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7700    0.9087   -2.9965 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1715    2.2410   -1.7710 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4999    1.8182   -2.1649 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4901   -0.4912   -2.1959 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6195   -1.8288   -1.5560 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  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
 10 12  2  0  0  0  0
 12 13  1  0  0  0  0
 13 14  2  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
 19 20  1  0  0  0  0
 20 21  1  0  0  0  0
 20 22  1  0  0  0  0
 22 23  1  0  0  0  0
 22 24  1  0  0  0  0
 22 25  1  1  0  0  0
 25 26  2  0  0  0  0
 25 27  1  0  0  0  0
 19 28  1  0  0  0  0
 28 29  1  0  0  0  0
 15 30  1  0  0  0  0
 30 31  1  0  0  0  0
 12  6  1  0  0  0  0
 31 13  1  0  0  0  0
 28 16  1  0  0  0  0
  1 32  1  0  0  0  0
  1 33  1  0  0  0  0
  1 34  1  0  0  0  0
  2 35  1  0  0  0  0
  2 36  1  0  0  0  0
  3 37  1  0  0  0  0
  3 38  1  0  0  0  0
  4 39  1  0  0  0  0
  4 40  1  0  0  0  0
  5 41  1  0  0  0  0
  5 42  1  0  0  0  0
  7 43  1  0  0  0  0
  8 44  1  0  0  0  0
  9 45  1  0  0  0  0
 11 46  1  0  0  0  0
 15 47  1  1  0  0  0
 16 48  1  6  0  0  0
 18 49  1  0  0  0  0
 18 50  1  0  0  0  0
 19 51  1  1  0  0  0
 20 52  1  6  0  0  0
 21 53  1  0  0  0  0
 23 54  1  0  0  0  0
 23 55  1  0  0  0  0
 23 56  1  0  0  0  0
 24 57  1  0  0  0  0
 24 58  1  0  0  0  0
 24 59  1  0  0  0  0
 27 60  1  0  0  0  0
 29 61  1  0  0  0  0
 29 62  1  0  0  0  0
 29 63  1  0  0  0  0
 30 64  1  0  0  0  0
 30 65  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0003135

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H]OC(=O)C(C([H])([H])[H])(C([H])([H])[H])[C@]([H])(O[H])[C@@]1([H])N(C([H])([H])[H])[C@@]([H])(SC1([H])[H])[C@]1([H])N=C(SC1([H])[H])C1=C(O[H])C([H])=C([H])C([H])=C1C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])[H]

> <INCHI_IDENTIFIER>
InChI=1S/C23H34N2O4S2/c1-5-6-7-9-14-10-8-11-17(26)18(14)20-24-15(12-30-20)21-25(4)16(13-31-21)19(27)23(2,3)22(28)29/h8,10-11,15-16,19,21,26-27H,5-7,9,12-13H2,1-4H3,(H,28,29)/t15-,16+,19-,21+/m1/s1

> <INCHI_KEY>
QZBCDLLHQSDFIG-ZEVBXJOLSA-N

> <FORMULA>
C23H34N2O4S2

> <MOLECULAR_WEIGHT>
466.66

> <EXACT_MASS>
466.195999931

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
65

> <JCHEM_AVERAGE_POLARIZABILITY>
51.798927726241814

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(3S)-3-hydroxy-3-[(2S,4R)-2-[(4R)-2-(2-hydroxy-6-pentylphenyl)-4,5-dihydro-1,3-thiazol-4-yl]-3-methyl-1,3-thiazolidin-4-yl]-2,2-dimethylpropanoic acid

> <ALOGPS_LOGP>
3.51

> <JCHEM_LOGP>
3.43974623560951

> <ALOGPS_LOGS>
-4.56

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
10.719910167908875

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.6773937034026742

> <JCHEM_PKA_STRONGEST_BASIC>
6.459370058018862

> <JCHEM_POLAR_SURFACE_AREA>
93.36000000000001

> <JCHEM_REFRACTIVITY>
128.31009999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
9

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.28e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(3S)-3-hydroxy-3-[(2S,4R)-2-[(4R)-2-(2-hydroxy-6-pentylphenyl)-4,5-dihydro-1,3-thiazol-4-yl]-3-methyl-1,3-thiazolidin-4-yl]-2,2-dimethylpropanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$

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       8.449  -0.428  -0.111  0.00  0.00           C+0
HETATM    2  C   UNK     0       7.178   0.221  -0.645  0.00  0.00           C+0
HETATM    3  C   UNK     0       5.995  -0.683  -0.470  0.00  0.00           C+0
HETATM    4  C   UNK     0       4.693  -0.096  -0.969  0.00  0.00           C+0
HETATM    5  C   UNK     0       4.246   1.138  -0.233  0.00  0.00           C+0
HETATM    6  C   UNK     0       3.930   0.872   1.193  0.00  0.00           C+0
HETATM    7  C   UNK     0       4.916   1.177   2.139  0.00  0.00           C+0
HETATM    8  C   UNK     0       4.759   0.924   3.478  0.00  0.00           C+0
HETATM    9  C   UNK     0       3.579   0.353   3.856  0.00  0.00           C+0
HETATM   10  C   UNK     0       2.567   0.031   2.958  0.00  0.00           C+0
HETATM   11  O   UNK     0       1.416  -0.536   3.390  0.00  0.00           O+0
HETATM   12  C   UNK     0       2.757   0.304   1.594  0.00  0.00           C+0
HETATM   13  C   UNK     0       1.660   0.036   0.650  0.00  0.00           C+0
HETATM   14  N   UNK     0       0.541  -0.517   0.937  0.00  0.00           N+0
HETATM   15  C   UNK     0      -0.430  -0.722  -0.032  0.00  0.00           C+0
HETATM   16  C   UNK     0      -1.335   0.489  -0.102  0.00  0.00           C+0
HETATM   17  S   UNK     0      -2.160   0.793   1.502  0.00  0.00           S+0
HETATM   18  C   UNK     0      -3.850   0.323   0.927  0.00  0.00           C+0
HETATM   19  C   UNK     0      -3.563  -0.169  -0.438  0.00  0.00           C+0
HETATM   20  C   UNK     0      -4.759   0.062  -1.309  0.00  0.00           C+0
HETATM   21  O   UNK     0      -4.596  -0.488  -2.585  0.00  0.00           O+0
HETATM   22  C   UNK     0      -6.069  -0.395  -0.754  0.00  0.00           C+0
HETATM   23  C   UNK     0      -6.084  -1.880  -0.453  0.00  0.00           C+0
HETATM   24  C   UNK     0      -7.072  -0.240  -1.932  0.00  0.00           C+0
HETATM   25  C   UNK     0      -6.635   0.430   0.321  0.00  0.00           C+0
HETATM   26  O   UNK     0      -6.989   1.611   0.101  0.00  0.00           O+0
HETATM   27  O   UNK     0      -6.789  -0.078   1.593  0.00  0.00           O+0
HETATM   28  N   UNK     0      -2.402   0.398  -0.990  0.00  0.00           N+0
HETATM   29  C   UNK     0      -2.527   1.375  -1.996  0.00  0.00           C+0
HETATM   30  C   UNK     0       0.190  -0.838  -1.421  0.00  0.00           C+0
HETATM   31  S   UNK     0       1.510   0.412  -1.093  0.00  0.00           S+0
HETATM   32  H   UNK     0       8.465  -0.270   0.981  0.00  0.00           H+0
HETATM   33  H   UNK     0       9.304   0.106  -0.598  0.00  0.00           H+0
HETATM   34  H   UNK     0       8.402  -1.486  -0.405  0.00  0.00           H+0
HETATM   35  H   UNK     0       7.290   0.465  -1.729  0.00  0.00           H+0
HETATM   36  H   UNK     0       7.023   1.150  -0.086  0.00  0.00           H+0
HETATM   37  H   UNK     0       6.180  -1.575  -1.139  0.00  0.00           H+0
HETATM   38  H   UNK     0       5.908  -1.101   0.544  0.00  0.00           H+0
HETATM   39  H   UNK     0       3.975  -0.943  -0.930  0.00  0.00           H+0
HETATM   40  H   UNK     0       4.842   0.163  -2.025  0.00  0.00           H+0
HETATM   41  H   UNK     0       3.460   1.624  -0.766  0.00  0.00           H+0
HETATM   42  H   UNK     0       5.133   1.852  -0.283  0.00  0.00           H+0
HETATM   43  H   UNK     0       5.830   1.637   1.813  0.00  0.00           H+0
HETATM   44  H   UNK     0       5.524   1.160   4.217  0.00  0.00           H+0
HETATM   45  H   UNK     0       3.377   0.118   4.909  0.00  0.00           H+0
HETATM   46  H   UNK     0       0.585  -0.860   3.081  0.00  0.00           H+0
HETATM   47  H   UNK     0      -1.002  -1.644   0.220  0.00  0.00           H+0
HETATM   48  H   UNK     0      -0.696   1.366  -0.324  0.00  0.00           H+0
HETATM   49  H   UNK     0      -4.126  -0.517   1.601  0.00  0.00           H+0
HETATM   50  H   UNK     0      -4.439   1.228   1.027  0.00  0.00           H+0
HETATM   51  H   UNK     0      -3.412  -1.290  -0.420  0.00  0.00           H+0
HETATM   52  H   UNK     0      -4.883   1.171  -1.499  0.00  0.00           H+0
HETATM   53  H   UNK     0      -4.512  -1.472  -2.562  0.00  0.00           H+0
HETATM   54  H   UNK     0      -5.284  -2.195   0.220  0.00  0.00           H+0
HETATM   55  H   UNK     0      -6.102  -2.405  -1.429  0.00  0.00           H+0
HETATM   56  H   UNK     0      -7.052  -2.088   0.053  0.00  0.00           H+0
HETATM   57  H   UNK     0      -7.157   0.858  -2.063  0.00  0.00           H+0
HETATM   58  H   UNK     0      -6.685  -0.721  -2.837  0.00  0.00           H+0
HETATM   59  H   UNK     0      -8.066  -0.608  -1.626  0.00  0.00           H+0
HETATM   60  H   UNK     0      -7.694  -0.257   2.012  0.00  0.00           H+0
HETATM   61  H   UNK     0      -2.770   0.909  -2.997  0.00  0.00           H+0
HETATM   62  H   UNK     0      -3.172   2.241  -1.771  0.00  0.00           H+0
HETATM   63  H   UNK     0      -1.500   1.818  -2.165  0.00  0.00           H+0
HETATM   64  H   UNK     0      -0.490  -0.491  -2.196  0.00  0.00           H+0
HETATM   65  H   UNK     0       0.620  -1.829  -1.556  0.00  0.00           H+0
CONECT    1    2   32   33   34                                             
CONECT    2    1    3   35   36                                             
CONECT    3    2    4   37   38                                             
CONECT    4    3    5   39   40                                             
CONECT    5    4    6   41   42                                             
CONECT    6    5    7   12                                                  
CONECT    7    6    8   43                                                  
CONECT    8    7    9   44                                                  
CONECT    9    8   10   45                                                  
CONECT   10    9   11   12                                                  
CONECT   11   10   46                                                       
CONECT   12   10   13    6                                                  
CONECT   13   12   14   31                                                  
CONECT   14   13   15                                                       
CONECT   15   14   16   30   47                                             
CONECT   16   15   17   28   48                                             
CONECT   17   16   18                                                       
CONECT   18   17   19   49   50                                             
CONECT   19   18   20   28   51                                             
CONECT   20   19   21   22   52                                             
CONECT   21   20   53                                                       
CONECT   22   20   23   24   25                                             
CONECT   23   22   54   55   56                                             
CONECT   24   22   57   58   59                                             
CONECT   25   22   26   27                                                  
CONECT   26   25                                                            
CONECT   27   25   60                                                       
CONECT   28   19   29   16                                                  
CONECT   29   28   61   62   63                                             
CONECT   30   15   31   64   65                                             
CONECT   31   30   13                                                       
CONECT   32    1                                                            
CONECT   33    1                                                            
CONECT   34    1                                                            
CONECT   35    2                                                            
CONECT   36    2                                                            
CONECT   37    3                                                            
CONECT   38    3                                                            
CONECT   39    4                                                            
CONECT   40    4                                                            
CONECT   41    5                                                            
CONECT   42    5                                                            
CONECT   43    7                                                            
CONECT   44    8                                                            
CONECT   45    9                                                            
CONECT   46   11                                                            
CONECT   47   15                                                            
CONECT   48   16                                                            
CONECT   49   18                                                            
CONECT   50   18                                                            
CONECT   51   19                                                            
CONECT   52   20                                                            
CONECT   53   21                                                            
CONECT   54   23                                                            
CONECT   55   23                                                            
CONECT   56   23                                                            
CONECT   57   24                                                            
CONECT   58   24                                                            
CONECT   59   24                                                            
CONECT   60   27                                                            
CONECT   61   29                                                            
CONECT   62   29                                                            
CONECT   63   29                                                            
CONECT   64   30                                                            
CONECT   65   30                                                            
MASTER        0    0    0    0    0    0    0    0   65    0  134    0
END

Mrv1652306242117453D

65 67  0  0  0  0            999 V2000
    8.4489   -0.4281   -0.1109 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1776    0.2212   -0.6448 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.9951   -0.6832   -0.4701 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.6931   -0.0958   -0.9693 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.2463    1.1382   -0.2333 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.9299    0.8721    1.1934 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9160    1.1774    2.1386 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7590    0.9244    3.4780 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5795    0.3528    3.8556 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5670    0.0312    2.9584 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4158   -0.5358    3.3898 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7568    0.3035    1.5937 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6599    0.0362    0.6502 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5405   -0.5169    0.9371 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4301   -0.7221   -0.0318 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.3355    0.4888   -0.1020 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.1602    0.7926    1.5024 S   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8499    0.3230    0.9266 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.5630   -0.1687   -0.4382 C   0  0  1  0  0  0  0  0  0  0  0  0
   -4.7589    0.0620   -1.3094 C   0  0  1  0  0  0  0  0  0  0  0  0
   -4.5962   -0.4876   -2.5853 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0689   -0.3948   -0.7541 C   0  0  2  0  0  0  0  0  0  0  0  0
   -6.0842   -1.8804   -0.4529 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0716   -0.2399   -1.9320 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.6351    0.4302    0.3213 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.9890    1.6109    0.1009 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7885   -0.0781    1.5933 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4019    0.3976   -0.9898 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5265    1.3748   -1.9965 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1903   -0.8379   -1.4213 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.5095    0.4119   -1.0935 S   0  0  0  0  0  0  0  0  0  0  0  0
    8.4650   -0.2699    0.9807 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.3036    0.1061   -0.5978 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.4016   -1.4861   -0.4045 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.2900    0.4652   -1.7287 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.0232    1.1500   -0.0858 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.1797   -1.5746   -1.1389 H   0  0  0  0  0  0  0  0  0  0  0  0
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    4.8420    0.1630   -2.0252 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4599    1.6238   -0.7655 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1334    1.8521   -0.2828 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8297    1.6373    1.8132 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5243    1.1604    4.2172 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3771    0.1182    4.9085 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5854   -0.8601    3.0812 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0024   -1.6437    0.2196 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6964    1.3660   -0.3237 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1264   -0.5166    1.6006 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4395    1.2283    1.0272 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4121   -1.2899   -0.4197 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8829    1.1714   -1.4988 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5121   -1.4718   -2.5616 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2840   -2.1946    0.2201 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1017   -2.4045   -1.4291 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0523   -2.0879    0.0531 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1570    0.8581   -2.0633 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.6848   -0.7206   -2.8366 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.0660   -0.6076   -1.6257 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.6940   -0.2565    2.0121 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7700    0.9087   -2.9965 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1715    2.2410   -1.7710 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4999    1.8182   -2.1649 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4901   -0.4912   -2.1959 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6195   -1.8288   -1.5560 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
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  3  4  1  0  0  0  0
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M  END
> <DATABASE_ID>
NP0003135

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H]OC(=O)C(C([H])([H])[H])(C([H])([H])[H])[C@]([H])(O[H])[C@@]1([H])N(C([H])([H])[H])[C@@]([H])(SC1([H])[H])[C@]1([H])N=C(SC1([H])[H])C1=C(O[H])C([H])=C([H])C([H])=C1C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])[H]

> <INCHI_IDENTIFIER>
InChI=1S/C23H34N2O4S2/c1-5-6-7-9-14-10-8-11-17(26)18(14)20-24-15(12-30-20)21-25(4)16(13-31-21)19(27)23(2,3)22(28)29/h8,10-11,15-16,19,21,26-27H,5-7,9,12-13H2,1-4H3,(H,28,29)/t15-,16+,19-,21+/m1/s1

> <INCHI_KEY>
QZBCDLLHQSDFIG-ZEVBXJOLSA-N

> <FORMULA>
C23H34N2O4S2

> <MOLECULAR_WEIGHT>
466.66

> <EXACT_MASS>
466.195999931

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
65

> <JCHEM_AVERAGE_POLARIZABILITY>
51.798927726241814

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(3S)-3-hydroxy-3-[(2S,4R)-2-[(4R)-2-(2-hydroxy-6-pentylphenyl)-4,5-dihydro-1,3-thiazol-4-yl]-3-methyl-1,3-thiazolidin-4-yl]-2,2-dimethylpropanoic acid

> <ALOGPS_LOGP>
3.51

> <JCHEM_LOGP>
3.43974623560951

> <ALOGPS_LOGS>
-4.56

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
10.719910167908875

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.6773937034026742

> <JCHEM_PKA_STRONGEST_BASIC>
6.459370058018862

> <JCHEM_POLAR_SURFACE_AREA>
93.36000000000001

> <JCHEM_REFRACTIVITY>
128.31009999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
9

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.28e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(3S)-3-hydroxy-3-[(2S,4R)-2-[(4R)-2-(2-hydroxy-6-pentylphenyl)-4,5-dihydro-1,3-thiazol-4-yl]-3-methyl-1,3-thiazolidin-4-yl]-2,2-dimethylpropanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$

View in JSmol View NMR Assignments

Synonyms

Not Available

Chemical Formula

C₂₃H₃₄N₂O₄S₂

Average Mass

466.6600 Da

Monoisotopic Mass

466.19600 Da

IUPAC Name

(3S)-3-hydroxy-3-[(2S,4R)-2-[(4R)-2-(2-hydroxy-6-pentylphenyl)-4,5-dihydro-1,3-thiazol-4-yl]-3-methyl-1,3-thiazolidin-4-yl]-2,2-dimethylpropanoic acid

Traditional Name

(3S)-3-hydroxy-3-[(2S,4R)-2-[(4R)-2-(2-hydroxy-6-pentylphenyl)-4,5-dihydro-1,3-thiazol-4-yl]-3-methyl-1,3-thiazolidin-4-yl]-2,2-dimethylpropanoic acid

CAS Registry Number

Not Available

SMILES

CCCCCC1=C(C2=N[C@H](CS2)[C@@H]2SC[C@@H]([C@@H](O)C(C)(C)C(O)=O)N2C)C(O)=CC=C1

InChI Identifier

InChI=1S/C23H34N2O4S2/c1-5-6-7-9-14-10-8-11-17(26)18(14)20-24-15(12-30-20)21-25(4)16(13-31-21)19(27)23(2,3)22(28)29/h8,10-11,15-16,19,21,26-27H,5-7,9,12-13H2,1-4H3,(H,28,29)/t15-,16+,19-,21+/m1/s1

InChI Key

QZBCDLLHQSDFIG-ZEVBXJOLSA-N

Spectra

Spectrum Type	Description	Depositor ID	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 25 MHz, D₂O, predicted)	Wishart Lab	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Wishart Lab	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Wishart Lab	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Wishart Lab	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Wishart Lab	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Wishart Lab	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Wishart Lab	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Wishart Lab	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Wishart Lab	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Wishart Lab	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Wishart Lab	2021-06-20	View Spectrum

Species

Species of Origin

Species Name	Source	Reference
Agrobacterium		10656570

Species Where Detected

Species Name	Source	Reference
Agrobacterium sp.	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	3.51	ALOGPS
logP	3.44	ChemAxon
logS	-4.6	ALOGPS
pKa (Strongest Acidic)	3.68	ChemAxon
pKa (Strongest Basic)	6.46	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	93.36 Å²	ChemAxon
Rotatable Bond Count	9	ChemAxon
Refractivity	128.31 m³·mol⁻¹	ChemAxon
Polarizability	51.8 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	ChemAxon

External Links

NPAtlas ID

NPA017357

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

C00015420

Chemspider ID

24603368

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

Not Available

PDB ID

Not Available

ChEBI ID

65375

Good Scents ID

Not Available

References

General References

Acebal C, Canedo LM, Puentes JL, Baz JP, Romero F, de la Calle F, Gravalos MD, Rodriguez P: Agrochelin, a new cytotoxic antibiotic from a marine Agrobacterium. Taxonomy, fermentation, isolation, physico-chemical properties and biological activity. J Antibiot (Tokyo). 1999 Nov;52(11):983-7. doi: 10.7164/antibiotics.52.983. [PubMed:10656570 ]
Diettrich J, Kage H, Nett M: Genomics-inspired discovery of massiliachelin, an agrochelin epimer from Massilia sp. NR 4-1. Beilstein J Org Chem. 2019 Jun 13;15:1298-1303. doi: 10.3762/bjoc.15.128. eCollection 2019. [PubMed:31293678 ]

Showing NP-Card for Agrochelin (NP0003135)

MOL for NP0003135 (Agrochelin)

3D MOL for NP0003135 (Agrochelin)

3D SDF for NP0003135 (Agrochelin)

3D-SDF for NP0003135 (Agrochelin)

PDB for NP0003135 (Agrochelin)

3D PDB for NP0003135 (Agrochelin)

SMILES for NP0003135 (Agrochelin)

INCHI for NP0003135 (Agrochelin)

Structure for NP0003135 (Agrochelin)

3D Structure for NP0003135 (Agrochelin)