NP-MRD: Showing NP-Card for (2s,4r)-4-ethyl-n-[(1r,2r)-2-hydroxy-1-[(2r,3r,4s,5r,6r)-3,4,5-trihydroxy-6-(methylsulfanyl)oxan-2-yl]propyl]-1-methylpyrrolidine-2-carboximidic acid (NP0260805)

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Record Information

Version

2.0

Created at

2022-09-08 03:04:14 UTC

Updated at

2022-09-08 03:04:14 UTC

NP-MRD ID

NP0260805

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(2s,4r)-4-ethyl-n-[(1r,2r)-2-hydroxy-1-[(2r,3r,4s,5r,6r)-3,4,5-trihydroxy-6-(methylsulfanyl)oxan-2-yl]propyl]-1-methylpyrrolidine-2-carboximidic acid

Description

Lincomycin-B belongs to the class of organic compounds known as proline and derivatives. Proline and derivatives are compounds containing proline or a derivative thereof resulting from reaction of proline at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom. (2s,4r)-4-ethyl-n-[(1r,2r)-2-hydroxy-1-[(2r,3r,4s,5r,6r)-3,4,5-trihydroxy-6-(methylsulfanyl)oxan-2-yl]propyl]-1-methylpyrrolidine-2-carboximidic acid is found in Streptomyces lincolnensis. (2s,4r)-4-ethyl-n-[(1r,2r)-2-hydroxy-1-[(2r,3r,4s,5r,6r)-3,4,5-trihydroxy-6-(methylsulfanyl)oxan-2-yl]propyl]-1-methylpyrrolidine-2-carboximidic acid was first documented in 2015 (PMID: 26248490). Based on a literature review a small amount of articles have been published on Lincomycin-B (PMID: 32816147) (PMID: 31916478).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309082205042D          

 26 27  0  0  1  0            999 V2000
    2.0367   -1.2991    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7512   -1.7116    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7512   -2.5366    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.4186   -3.0215    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1637   -3.8062    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.6486   -4.4736    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4691   -4.3874    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3130   -5.2273    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.7980   -5.8947    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.6184   -5.8085    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    5.1034   -6.4759    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9540   -5.0548    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4624   -6.6484    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.9473   -7.3158    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6118   -8.0695    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.0967   -8.7369    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    4.9172   -8.6507    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7913   -8.1557    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.4557   -8.9094    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3064   -7.4883    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.4859   -7.5745    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6419   -6.7346    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.1570   -6.0672    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3387   -3.8062    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.8538   -4.4736    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0837   -3.0215    0.0000 C   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
  5  6  1  1  0  0  0
  6  7  1  4  0  0  0
  6  8  2  0  0  0  0
  9  8  1  6  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 10 12  1  6  0  0  0
 13  9  1  1  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  6  0  0  0
 16 17  1  0  0  0  0
 15 18  1  0  0  0  0
 18 19  1  6  0  0  0
 18 20  1  0  0  0  0
 20 21  1  1  0  0  0
 20 22  1  0  0  0  0
 13 22  1  0  0  0  0
 22 23  1  1  0  0  0
  5 24  1  0  0  0  0
 24 25  1  0  0  0  0
 24 26  1  0  0  0  0
  3 26  1  0  0  0  0
M  END

     RDKit          3D

 58 59  0  0  0  0  0  0  0  0999 V2000
   -6.4632    1.3539    0.4907 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7261    0.0351    0.4907 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2665    0.3145    0.3087 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.4657   -0.9915    0.3006 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1088   -0.5363    0.7954 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.0944   -0.5313   -0.2626 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3201    0.2862   -1.3819 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0302   -1.2534   -0.1690 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.9953   -1.2769   -1.1915 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.2324   -2.7233   -1.5573 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.0726   -3.2227   -2.1898 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2100   -2.8553   -2.5418 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2526   -0.5752   -0.7455 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.9726    0.7271   -0.4557 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8226    1.3417    0.4258 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.8859    3.1161   -0.0444 S   0  0  0  0  0  0  0  0  0  0  0  0
    3.9929    3.9661    1.0881 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2107    0.8358    0.4486 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.9500    1.4408   -0.5843 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.3641   -0.6444    0.4309 C   0  0  1  0  0  0  0  0  0  0  0  0
    5.0973   -1.1472    1.4836 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9684   -1.2643    0.3573 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.3941   -1.0816    1.6064 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2898    0.7639    1.3941 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7220    1.8372    0.6382 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7098    0.9578    1.5778 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9140    2.1126    1.0766 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.4869    1.2315    0.9296 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5779    1.7242   -0.5623 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1132   -0.6301   -0.3007 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9122   -0.4519    1.4680 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0749    0.9131   -0.5863 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4418   -1.3905   -0.7119 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9660   -1.6486    1.0399 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8051   -1.2421    1.5819 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5153   -0.2280   -2.2441 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5865   -0.7813   -2.0956 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4131   -3.3415   -0.6736 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2069   -2.8015   -3.2066 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0383   -4.3196   -2.3176 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9248   -3.0433   -1.5325 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8665   -3.5359   -2.1948 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9387   -0.5776   -1.6413 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3906    1.3083    1.4297 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8386    4.4718    0.5607 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4741    4.7803    1.6482 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4658    3.2677    1.8077 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6952    1.2063    1.3994 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.9071    1.3071   -0.3474 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8473   -0.9215   -0.5514 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.9664   -1.4771    1.1337 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1081   -2.3299    0.1852 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0914   -1.3457    2.2769 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7340    2.7440    1.2984 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6616    1.6451    0.4019 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3065    2.1046   -0.2599 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1088    0.3508    2.4198 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9575    2.0261    1.6480 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5 24  1  0
 24 25  1  0
 24 26  1  0
  5  6  1  0
  6  7  1  0
  6  8  2  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 10 12  1  0
  9 13  1  0
 13 14  1  0
 14 15  1  0
 15 16  1  0
 16 17  1  0
 15 18  1  0
 18 19  1  0
 18 20  1  0
 20 21  1  0
 20 22  1  0
 22 23  1  0
 26  3  1  0
 22 13  1  0
  1 27  1  0
  1 28  1  0
  1 29  1  0
  2 30  1  0
  2 31  1  0
  3 32  1  6
  4 33  1  0
  4 34  1  0
  5 35  1  1
 25 54  1  0
 25 55  1  0
 25 56  1  0
 26 57  1  0
 26 58  1  0
  7 36  1  0
  9 37  1  6
 10 38  1  1
 11 39  1  0
 11 40  1  0
 11 41  1  0
 12 42  1  0
 13 43  1  6
 15 44  1  1
 17 45  1  0
 17 46  1  0
 17 47  1  0
 18 48  1  1
 19 49  1  0
 20 50  1  6
 21 51  1  0
 22 52  1  6
 23 53  1  0
M  END


  Mrv1652309082205042D          

 26 27  0  0  1  0            999 V2000
    2.0367   -1.2991    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7512   -1.7116    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7512   -2.5366    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.4186   -3.0215    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1637   -3.8062    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.6486   -4.4736    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4691   -4.3874    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3130   -5.2273    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.7980   -5.8947    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.6184   -5.8085    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    5.1034   -6.4759    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9540   -5.0548    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4624   -6.6484    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.9473   -7.3158    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6118   -8.0695    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.0967   -8.7369    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    4.9172   -8.6507    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7913   -8.1557    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.4557   -8.9094    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3064   -7.4883    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.4859   -7.5745    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6419   -6.7346    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.1570   -6.0672    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3387   -3.8062    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.8538   -4.4736    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0837   -3.0215    0.0000 C   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
  5  6  1  1  0  0  0
  6  7  1  4  0  0  0
  6  8  2  0  0  0  0
  9  8  1  6  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 10 12  1  6  0  0  0
 13  9  1  1  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  6  0  0  0
 16 17  1  0  0  0  0
 15 18  1  0  0  0  0
 18 19  1  6  0  0  0
 18 20  1  0  0  0  0
 20 21  1  1  0  0  0
 20 22  1  0  0  0  0
 13 22  1  0  0  0  0
 22 23  1  1  0  0  0
  5 24  1  0  0  0  0
 24 25  1  0  0  0  0
 24 26  1  0  0  0  0
  3 26  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0260805

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC[C@@H]1C[C@H](N(C)C1)C(O)=N[C@H]([C@@H](C)O)[C@H]1O[C@H](SC)[C@H](O)[C@@H](O)[C@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C17H32N2O6S/c1-5-9-6-10(19(3)7-9)16(24)18-11(8(2)20)15-13(22)12(21)14(23)17(25-15)26-4/h8-15,17,20-23H,5-7H2,1-4H3,(H,18,24)/t8-,9-,10+,11-,12+,13-,14-,15-,17-/m1/s1

> <INCHI_KEY>
DZSDDKNXMARQMJ-AVXYAQEDSA-N

> <FORMULA>
C17H32N2O6S

> <MOLECULAR_WEIGHT>
392.51

> <EXACT_MASS>
392.198107932

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_ATOM_COUNT>
58

> <JCHEM_AVERAGE_POLARIZABILITY>
41.37939807221299

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S,4R)-4-ethyl-N-[(1R,2R)-2-hydroxy-1-[(2R,3R,4S,5R,6R)-3,4,5-trihydroxy-6-(methylsulfanyl)oxan-2-yl]propyl]-1-methylpyrrolidine-2-carboximidic acid

> <JCHEM_LOGP>
-2.6204544383501873

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
12.495570463423594

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.197296684760967

> <JCHEM_PKA_STRONGEST_BASIC>
8.360079842397585

> <JCHEM_POLAR_SURFACE_AREA>
125.98000000000002

> <JCHEM_REFRACTIVITY>
98.58700000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(2S,4R)-4-ethyl-N-[(1R,2R)-2-hydroxy-1-[(2R,3R,4S,5R,6R)-3,4,5-trihydroxy-6-(methylsulfanyl)oxan-2-yl]propyl]-1-methylpyrrolidine-2-carboximidic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 08-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   08-SEP-22         0                                  
HETATM    1  C   UNK     0       3.802  -2.425   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       5.136  -3.195   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       5.136  -4.735   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       6.381  -5.640   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       5.906  -7.105   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       6.811  -8.351   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       8.342  -8.190   0.000  0.00  0.00           O+0
HETATM    8  N   UNK     0       6.184  -9.758   0.000  0.00  0.00           N+0
HETATM    9  C   UNK     0       7.090 -11.003   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       8.621 -10.842   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       9.526 -12.088   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       9.247  -9.436   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0       6.463 -12.410   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0       7.368 -13.656   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0       6.742 -15.063   0.000  0.00  0.00           C+0
HETATM   16  S   UNK     0       7.647 -16.309   0.000  0.00  0.00           S+0
HETATM   17  C   UNK     0       9.179 -16.148   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       5.210 -15.224   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0       4.584 -16.631   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0       4.305 -13.978   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0       2.774 -14.139   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0       4.932 -12.571   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0       4.026 -11.325   0.000  0.00  0.00           O+0
HETATM   24  N   UNK     0       4.366  -7.105   0.000  0.00  0.00           N+0
HETATM   25  C   UNK     0       3.460  -8.351   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       3.890  -5.640   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4   26                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6   24                                                  
CONECT    6    5    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    9                                                       
CONECT    9    8   10   13                                                  
CONECT   10    9   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10                                                            
CONECT   13    9   14   22                                                  
CONECT   14   13   15                                                       
CONECT   15   14   16   18                                                  
CONECT   16   15   17                                                       
CONECT   17   16                                                            
CONECT   18   15   19   20                                                  
CONECT   19   18                                                            
CONECT   20   18   21   22                                                  
CONECT   21   20                                                            
CONECT   22   20   13   23                                                  
CONECT   23   22                                                            
CONECT   24    5   25   26                                                  
CONECT   25   24                                                            
CONECT   26   24    3                                                       
MASTER        0    0    0    0    0    0    0    0   26    0   54    0
END

View in JSmol

Synonyms

Value	Source
Lincomycin b	MeSH
Lincomycin b hydrochloride	MeSH

Chemical Formula

C₁₇H₃₂N₂O₆S

Average Mass

392.5100 Da

Monoisotopic Mass

392.19811 Da

IUPAC Name

(2S,4R)-4-ethyl-N-[(1R,2R)-2-hydroxy-1-[(2R,3R,4S,5R,6R)-3,4,5-trihydroxy-6-(methylsulfanyl)oxan-2-yl]propyl]-1-methylpyrrolidine-2-carboximidic acid

Traditional Name

(2S,4R)-4-ethyl-N-[(1R,2R)-2-hydroxy-1-[(2R,3R,4S,5R,6R)-3,4,5-trihydroxy-6-(methylsulfanyl)oxan-2-yl]propyl]-1-methylpyrrolidine-2-carboximidic acid

CAS Registry Number

Not Available

SMILES

CC[C@@H]1C[C@H](N(C)C1)C(O)=N[C@H]([C@@H](C)O)[C@H]1O[C@H](SC)[C@H](O)[C@@H](O)[C@H]1O

InChI Identifier

InChI=1S/C17H32N2O6S/c1-5-9-6-10(19(3)7-9)16(24)18-11(8(2)20)15-13(22)12(21)14(23)17(25-15)26-4/h8-15,17,20-23H,5-7H2,1-4H3,(H,18,24)/t8-,9-,10+,11-,12+,13-,14-,15-,17-/m1/s1

InChI Key

DZSDDKNXMARQMJ-AVXYAQEDSA-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

Species Name	Source	Reference
Streptomyces lincolnensis	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as proline and derivatives. Proline and derivatives are compounds containing proline or a derivative thereof resulting from reaction of proline at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

Proline and derivatives

Alternative Parents

Substituents

Proline or derivatives
Alpha-amino acid amide
Glycosyl compound
S-glycosyl compound
Pyrrolidine carboxylic acid or derivatives
Pyrrolidine-2-carboxamide
Monosaccharide
Oxane
N-alkylpyrrolidine
Monothioacetal
Pyrrolidine
Tertiary aliphatic amine
Tertiary amine
Secondary carboxylic acid amide
Secondary alcohol
Carboxamide group
Sulfenyl compound
Organoheterocyclic compound
Polyol
Oxacycle
Azacycle
Organooxygen compound
Organonitrogen compound
Alcohol
Organic oxide
Organic oxygen compound
Organosulfur compound
Hydrocarbon derivative
Organic nitrogen compound
Amine
Carbonyl group
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic 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	-2.6	ChemAxon
pKa (Strongest Acidic)	3.2	ChemAxon
pKa (Strongest Basic)	8.36	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	8	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	125.98 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	98.59 m³·mol⁻¹	ChemAxon
Polarizability	41.38 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	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

16736794

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

20055410

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Shen S, Li W: The inhibitory effects of metabolites from Bacillus pumilus on potato virus Y and the induction of early response genes in Nicotiana tabacum. AMB Express. 2020 Aug 20;10(1):152. doi: 10.1186/s13568-020-01089-1. [PubMed:32816147 ]
Yang J, Ye R, Zhang H, Liu Y: Amplification of lmbB1 gene in Streptomyces lincolnensis improves quantity and quality of lincomycin A fermentation. Prep Biochem Biotechnol. 2020;50(6):529-537. doi: 10.1080/10826068.2019.1710714. Epub 2020 Jan 9. [PubMed:31916478 ]
Pang AP, Du L, Lin CY, Qiao J, Zhao GR: Co-overexpression of lmbW and metK led to increased lincomycin A production and decreased byproduct lincomycin B content in an industrial strain of Streptomyces lincolnensis. J Appl Microbiol. 2015 Oct;119(4):1064-74. doi: 10.1111/jam.12919. [PubMed:26248490 ]
LOTUS database [Link]

Showing NP-Card for (2s,4r)-4-ethyl-n-[(1r,2r)-2-hydroxy-1-[(2r,3r,4s,5r,6r)-3,4,5-trihydroxy-6-(methylsulfanyl)oxan-2-yl]propyl]-1-methylpyrrolidine-2-carboximidic acid (NP0260805)

MOL for NP0260805 ((2s,4r)-4-ethyl-n-[(1r,2r)-2-hydroxy-1-[(2r,3r,4s,5r,6r)-3,4,5-trihydroxy-6-(methylsulfanyl)oxan-2-yl]propyl]-1-methylpyrrolidine-2-carboximidic acid)

3D MOL for NP0260805 ((2s,4r)-4-ethyl-n-[(1r,2r)-2-hydroxy-1-[(2r,3r,4s,5r,6r)-3,4,5-trihydroxy-6-(methylsulfanyl)oxan-2-yl]propyl]-1-methylpyrrolidine-2-carboximidic acid)

3D SDF for NP0260805 ((2s,4r)-4-ethyl-n-[(1r,2r)-2-hydroxy-1-[(2r,3r,4s,5r,6r)-3,4,5-trihydroxy-6-(methylsulfanyl)oxan-2-yl]propyl]-1-methylpyrrolidine-2-carboximidic acid)

3D-SDF for NP0260805 ((2s,4r)-4-ethyl-n-[(1r,2r)-2-hydroxy-1-[(2r,3r,4s,5r,6r)-3,4,5-trihydroxy-6-(methylsulfanyl)oxan-2-yl]propyl]-1-methylpyrrolidine-2-carboximidic acid)

PDB for NP0260805 ((2s,4r)-4-ethyl-n-[(1r,2r)-2-hydroxy-1-[(2r,3r,4s,5r,6r)-3,4,5-trihydroxy-6-(methylsulfanyl)oxan-2-yl]propyl]-1-methylpyrrolidine-2-carboximidic acid)

3D PDB for NP0260805 ((2s,4r)-4-ethyl-n-[(1r,2r)-2-hydroxy-1-[(2r,3r,4s,5r,6r)-3,4,5-trihydroxy-6-(methylsulfanyl)oxan-2-yl]propyl]-1-methylpyrrolidine-2-carboximidic acid)

SMILES for NP0260805 ((2s,4r)-4-ethyl-n-[(1r,2r)-2-hydroxy-1-[(2r,3r,4s,5r,6r)-3,4,5-trihydroxy-6-(methylsulfanyl)oxan-2-yl]propyl]-1-methylpyrrolidine-2-carboximidic acid)

INCHI for NP0260805 ((2s,4r)-4-ethyl-n-[(1r,2r)-2-hydroxy-1-[(2r,3r,4s,5r,6r)-3,4,5-trihydroxy-6-(methylsulfanyl)oxan-2-yl]propyl]-1-methylpyrrolidine-2-carboximidic acid)

Structure for NP0260805 ((2s,4r)-4-ethyl-n-[(1r,2r)-2-hydroxy-1-[(2r,3r,4s,5r,6r)-3,4,5-trihydroxy-6-(methylsulfanyl)oxan-2-yl]propyl]-1-methylpyrrolidine-2-carboximidic acid)

3D Structure for NP0260805 ((2s,4r)-4-ethyl-n-[(1r,2r)-2-hydroxy-1-[(2r,3r,4s,5r,6r)-3,4,5-trihydroxy-6-(methylsulfanyl)oxan-2-yl]propyl]-1-methylpyrrolidine-2-carboximidic acid)