NP-MRD: Showing NP-Card for (2s,4r)-n-[(1s)-2-hydroxy-1-[(3r,4s,5r,6r)-3,4,5-trihydroxy-6-(methylsulfanyl)oxan-2-yl]propyl]-1-methyl-4-propylpyrrolidine-2-carboximidic acid (NP0172632)

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Record Information

Version

2.0

Created at

2022-09-03 09:35:49 UTC

Updated at

2022-09-03 09:35:49 UTC

NP-MRD ID

NP0172632

Secondary Accession Numbers

None

Natural Product Identification

Common Name

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

Description

Lincomycin A, also known as epilincomycin or lincolnensin, 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)-n-[(1s)-2-hydroxy-1-[(3r,4s,5r,6r)-3,4,5-trihydroxy-6-(methylsulfanyl)oxan-2-yl]propyl]-1-methyl-4-propylpyrrolidine-2-carboximidic acid is found in Streptomyces lincolnensis. (2s,4r)-n-[(1s)-2-hydroxy-1-[(3r,4s,5r,6r)-3,4,5-trihydroxy-6-(methylsulfanyl)oxan-2-yl]propyl]-1-methyl-4-propylpyrrolidine-2-carboximidic acid was first documented in 2018 (PMID: 29792672). Based on a literature review a small amount of articles have been published on Lincomycin A (PMID: 31916478) (PMID: 32958639) (PMID: 30341075) (PMID: 29574602).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309032211352D          

 27 28  0  0  1  0            999 V2000
    2.0367   -0.4741    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    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  1  0  0  0  0  0  0  0  0  0
    4.6184   -5.8085    0.0000 C   0  0  0  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  0  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
  2  3  1  0  0  0  0
  4  3  1  6  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  1  0  0  0
  7  8  1  4  0  0  0
  7  9  2  0  0  0  0
 10  9  1  1  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 11 13  1  0  0  0  0
 10 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  6  0  0  0
 17 18  1  0  0  0  0
 16 19  1  0  0  0  0
 19 20  1  6  0  0  0
 19 21  1  0  0  0  0
 21 22  1  1  0  0  0
 21 23  1  0  0  0  0
 14 23  1  0  0  0  0
 23 24  1  1  0  0  0
  6 25  1  0  0  0  0
 25 26  1  0  0  0  0
 25 27  1  0  0  0  0
  4 27  1  0  0  0  0
M  END

     RDKit          3D

 61 62  0  0  0  0  0  0  0  0999 V2000
   -6.3137   -0.3974    1.2287 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2393    0.4898    0.0175 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4797   -0.0911   -1.1157 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0477   -0.4131   -0.8161 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.2356    0.7779   -0.3994 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9049    0.6270   -1.1058 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.7768    0.8667   -0.1714 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7417    2.1268    0.4211 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1205    0.0192    0.1050 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.1762    0.3443    1.0247 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.3717   -0.7682    2.0285 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.5152   -2.1171    1.3973 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3955   -0.4518    2.9161 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4842    0.6217    0.3478 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.9825   -0.4165   -0.3976 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.3195   -0.2392   -0.6537 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.3545   -0.7538    0.7665 S   0  0  0  0  0  0  0  0  0  0  0  0
    5.2161   -2.5460    1.0077 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7157    1.0913   -1.1892 C   0  0  2  0  0  0  0  0  0  0  0  0
    6.0561    1.3120   -0.8011 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9251    2.2572   -0.7083 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.0463    3.3014   -1.6224 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4602    1.8558   -0.5140 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.9682    1.5275   -1.7761 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9086   -0.7276   -1.6206 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6722   -1.7017   -0.5732 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3055   -0.9089   -2.0383 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3374   -0.6840    1.6290 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.9561   -1.2953    1.0220 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8435    0.1705    2.0237 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.2989    0.6308   -0.3346 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9012    1.4911    0.3328 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9738   -1.0699   -1.3769 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5565    0.5455   -1.9971 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9840   -1.2134   -0.0486 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6547    1.7461   -0.7110 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0513    0.7004    0.6919 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8163    1.3077   -1.9707 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4133    2.2945    1.1601 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9248    1.2564    1.6341 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4149   -0.7982    2.6269 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5300   -2.1064    0.2915 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6867   -2.8198    1.6731 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4355   -2.6002    1.8281 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0252    0.2328    3.5329 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2375    0.8280    1.1601 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5751   -0.9897   -1.4622 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3484   -2.8994    0.4108 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.1432   -3.0739    0.6855 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0277   -2.7757    2.0618 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7373    1.1210   -2.3069 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.1323    2.0484   -0.1568 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2597    2.6006    0.3094 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0476    4.1777   -1.1301 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9091    2.6948   -0.0499 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7003    1.0392   -2.2449 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3625   -2.5528   -0.6868 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6512   -2.0943   -0.7070 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8468   -1.2879    0.4448 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5335   -0.3147   -2.9398 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4357   -1.9960   -2.1817 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  6  1  0
  6 25  1  0
 25 26  1  0
 25 27  1  0
  6  7  1  0
  7  8  1  0
  7  9  2  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 11 13  1  0
 10 14  1  0
 14 15  1  0
 15 16  1  0
 16 17  1  0
 17 18  1  0
 16 19  1  0
 19 20  1  0
 19 21  1  0
 21 22  1  0
 21 23  1  0
 23 24  1  0
 27  4  1  0
 23 14  1  0
  1 28  1  0
  1 29  1  0
  1 30  1  0
  2 31  1  0
  2 32  1  0
  3 33  1  0
  3 34  1  0
  4 35  1  1
  5 36  1  0
  5 37  1  0
  6 38  1  6
 26 57  1  0
 26 58  1  0
 26 59  1  0
 27 60  1  0
 27 61  1  0
  8 39  1  0
 10 40  1  1
 11 41  1  1
 12 42  1  0
 12 43  1  0
 12 44  1  0
 13 45  1  0
 14 46  1  1
 16 47  1  6
 18 48  1  0
 18 49  1  0
 18 50  1  0
 19 51  1  6
 20 52  1  0
 21 53  1  1
 22 54  1  0
 23 55  1  1
 24 56  1  0
M  END


  Mrv1652309032211352D          

 27 28  0  0  1  0            999 V2000
    2.0367   -0.4741    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    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  1  0  0  0  0  0  0  0  0  0
    4.6184   -5.8085    0.0000 C   0  0  0  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  0  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
  2  3  1  0  0  0  0
  4  3  1  6  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  1  0  0  0
  7  8  1  4  0  0  0
  7  9  2  0  0  0  0
 10  9  1  1  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 11 13  1  0  0  0  0
 10 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  6  0  0  0
 17 18  1  0  0  0  0
 16 19  1  0  0  0  0
 19 20  1  6  0  0  0
 19 21  1  0  0  0  0
 21 22  1  1  0  0  0
 21 23  1  0  0  0  0
 14 23  1  0  0  0  0
 23 24  1  1  0  0  0
  6 25  1  0  0  0  0
 25 26  1  0  0  0  0
 25 27  1  0  0  0  0
  4 27  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0172632

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CCC[C@@H]1C[C@H](N(C)C1)C(O)=N[C@@H](C(C)O)C1O[C@H](SC)[C@H](O)[C@@H](O)[C@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C18H34N2O6S/c1-5-6-10-7-11(20(3)8-10)17(25)19-12(9(2)21)16-14(23)13(22)15(24)18(26-16)27-4/h9-16,18,21-24H,5-8H2,1-4H3,(H,19,25)/t9?,10-,11+,12+,13+,14-,15-,16?,18-/m1/s1

> <INCHI_KEY>
OJMMVQQUTAEWLP-ZUWRKQLMSA-N

> <FORMULA>
C18H34N2O6S

> <MOLECULAR_WEIGHT>
406.54

> <EXACT_MASS>
406.213757997

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_ATOM_COUNT>
61

> <JCHEM_AVERAGE_POLARIZABILITY>
43.39517110200933

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
0.34

> <JCHEM_LOGP>
-2.178002147595919

> <ALOGPS_LOGS>
-2.13

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
12.495573950929973

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.2357848279129864

> <JCHEM_PKA_STRONGEST_BASIC>
8.411435449256714

> <JCHEM_POLAR_SURFACE_AREA>
125.98000000000002

> <JCHEM_REFRACTIVITY>
103.18800000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.02e+00 g/l

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

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 03-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   03-SEP-22         0                                  
HETATM    1  C   UNK     0       3.802  -0.885   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       3.802  -2.425   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       5.136  -3.195   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       5.136  -4.735   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       6.381  -5.640   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       5.906  -7.105   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       6.811  -8.351   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       8.342  -8.190   0.000  0.00  0.00           O+0
HETATM    9  N   UNK     0       6.184  -9.758   0.000  0.00  0.00           N+0
HETATM   10  C   UNK     0       7.090 -11.003   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       8.621 -10.842   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       9.526 -12.088   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       9.247  -9.436   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0       6.463 -12.410   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0       7.368 -13.656   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0       6.742 -15.063   0.000  0.00  0.00           C+0
HETATM   17  S   UNK     0       7.647 -16.309   0.000  0.00  0.00           S+0
HETATM   18  C   UNK     0       9.179 -16.148   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       5.210 -15.224   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0       4.584 -16.631   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0       4.305 -13.978   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0       2.774 -14.139   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0       4.932 -12.571   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0       4.026 -11.325   0.000  0.00  0.00           O+0
HETATM   25  N   UNK     0       4.366  -7.105   0.000  0.00  0.00           N+0
HETATM   26  C   UNK     0       3.460  -8.351   0.000  0.00  0.00           C+0
HETATM   27  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                                                       
CONECT    4    3    5   27                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7   25                                                  
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10                                                       
CONECT   10    9   11   14                                                  
CONECT   11   10   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11                                                            
CONECT   14   10   15   23                                                  
CONECT   15   14   16                                                       
CONECT   16   15   17   19                                                  
CONECT   17   16   18                                                       
CONECT   18   17                                                            
CONECT   19   16   20   21                                                  
CONECT   20   19                                                            
CONECT   21   19   22   23                                                  
CONECT   22   21                                                            
CONECT   23   21   14   24                                                  
CONECT   24   23                                                            
CONECT   25    6   26   27                                                  
CONECT   26   25                                                            
CONECT   27   25    4                                                       
MASTER        0    0    0    0    0    0    0    0   27    0   56    0
END

View in JSmol

Synonyms

Value	Source
Lincolnensin	MeSH
Lincomycin monohydrochloride	MeSH
Lincomycin monohydrochloride, (2S-cis)-isomer	MeSH
Lincomycin monohydrochloride, hemihydrate	MeSH
Hemihydrate lincomycin monohydrochloride	MeSH
Lincocin	MeSH
Lincomycin monohydrochloride, (L-threo)-isomer	MeSH
Lincomycin, (L-threo)-isomer	MeSH
Epilincomycin	MeSH
Lincomycin	MeSH
Lincomycin hydrochloride	MeSH
Lincomycin, (2S-cis)-isomer	MeSH

Chemical Formula

C₁₈H₃₄N₂O₆S

Average Mass

406.5400 Da

Monoisotopic Mass

406.21376 Da

IUPAC Name

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

Traditional Name

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

CAS Registry Number

Not Available

SMILES

CCC[C@@H]1C[C@H](N(C)C1)C(O)=N[C@@H](C(C)O)C1O[C@H](SC)[C@H](O)[C@@H](O)[C@H]1O

InChI Identifier

InChI=1S/C18H34N2O6S/c1-5-6-10-7-11(20(3)8-10)17(25)19-12(9(2)21)16-14(23)13(22)15(24)18(26-16)27-4/h9-16,18,21-24H,5-8H2,1-4H3,(H,19,25)/t9?,10-,11+,12+,13+,14-,15-,16?,18-/m1/s1

InChI Key

OJMMVQQUTAEWLP-ZUWRKQLMSA-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
Azacycle
Organoheterocyclic compound
Oxacycle
Sulfenyl compound
Polyol
Hydrocarbon derivative
Organosulfur compound
Organooxygen compound
Organonitrogen compound
Alcohol
Organopnictogen compound
Organic oxygen compound
Organic oxide
Carbonyl group
Amine
Organic nitrogen compound
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	0.34	ALOGPS
logP	-2.2	ChemAxon
logS	-2.1	ALOGPS
pKa (Strongest Acidic)	3.24	ChemAxon
pKa (Strongest Basic)	8.41	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	7	ChemAxon
Refractivity	103.19 m³·mol⁻¹	ChemAxon
Polarizability	43.4 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

8710

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

9063

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

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 ]
Wang SA, Lin CI, Zhang J, Ushimaru R, Sasaki E, Liu HW: Studies of lincosamide formation complete the biosynthetic pathway for lincomycin A. Proc Natl Acad Sci U S A. 2020 Oct 6;117(40):24794-24801. doi: 10.1073/pnas.2009306117. Epub 2020 Sep 21. [PubMed:32958639 ]
Xu Y, Ke M, Li J, Tang Y, Wang N, Tan G, Wang Y, Liu R, Bai L, Zhang L, Wu H, Zhang B: TetR-Type Regulator SLCG_2919 Is a Negative Regulator of Lincomycin Biosynthesis in Streptomyces lincolnensis. Appl Environ Microbiol. 2018 Dec 13;85(1):e02091-18. doi: 10.1128/AEM.02091-18. Print 2019 Jan 1. [PubMed:30341075 ]
Zhang D, Tang Z, Liu W: Biosynthesis of Lincosamide Antibiotics: Reactions Associated with Degradation and Detoxification Pathways Play a Constructive Role. Acc Chem Res. 2018 Jun 19;51(6):1496-1506. doi: 10.1021/acs.accounts.8b00135. Epub 2018 May 24. [PubMed:29792672 ]
Xu Y, Tan G, Ke M, Li J, Tang Y, Meng S, Niu J, Wang Y, Liu R, Wu H, Bai L, Zhang L, Zhang B: Enhanced lincomycin production by co-overexpression of metK1 and metK2 in Streptomyces lincolnensis. J Ind Microbiol Biotechnol. 2018 May;45(5):345-355. doi: 10.1007/s10295-018-2029-1. Epub 2018 Mar 24. [PubMed:29574602 ]
LOTUS database [Link]

Showing NP-Card for (2s,4r)-n-[(1s)-2-hydroxy-1-[(3r,4s,5r,6r)-3,4,5-trihydroxy-6-(methylsulfanyl)oxan-2-yl]propyl]-1-methyl-4-propylpyrrolidine-2-carboximidic acid (NP0172632)

MOL for NP0172632 ((2s,4r)-n-[(1s)-2-hydroxy-1-[(3r,4s,5r,6r)-3,4,5-trihydroxy-6-(methylsulfanyl)oxan-2-yl]propyl]-1-methyl-4-propylpyrrolidine-2-carboximidic acid)

3D MOL for NP0172632 ((2s,4r)-n-[(1s)-2-hydroxy-1-[(3r,4s,5r,6r)-3,4,5-trihydroxy-6-(methylsulfanyl)oxan-2-yl]propyl]-1-methyl-4-propylpyrrolidine-2-carboximidic acid)

3D SDF for NP0172632 ((2s,4r)-n-[(1s)-2-hydroxy-1-[(3r,4s,5r,6r)-3,4,5-trihydroxy-6-(methylsulfanyl)oxan-2-yl]propyl]-1-methyl-4-propylpyrrolidine-2-carboximidic acid)

3D-SDF for NP0172632 ((2s,4r)-n-[(1s)-2-hydroxy-1-[(3r,4s,5r,6r)-3,4,5-trihydroxy-6-(methylsulfanyl)oxan-2-yl]propyl]-1-methyl-4-propylpyrrolidine-2-carboximidic acid)

PDB for NP0172632 ((2s,4r)-n-[(1s)-2-hydroxy-1-[(3r,4s,5r,6r)-3,4,5-trihydroxy-6-(methylsulfanyl)oxan-2-yl]propyl]-1-methyl-4-propylpyrrolidine-2-carboximidic acid)

3D PDB for NP0172632 ((2s,4r)-n-[(1s)-2-hydroxy-1-[(3r,4s,5r,6r)-3,4,5-trihydroxy-6-(methylsulfanyl)oxan-2-yl]propyl]-1-methyl-4-propylpyrrolidine-2-carboximidic acid)

SMILES for NP0172632 ((2s,4r)-n-[(1s)-2-hydroxy-1-[(3r,4s,5r,6r)-3,4,5-trihydroxy-6-(methylsulfanyl)oxan-2-yl]propyl]-1-methyl-4-propylpyrrolidine-2-carboximidic acid)

INCHI for NP0172632 ((2s,4r)-n-[(1s)-2-hydroxy-1-[(3r,4s,5r,6r)-3,4,5-trihydroxy-6-(methylsulfanyl)oxan-2-yl]propyl]-1-methyl-4-propylpyrrolidine-2-carboximidic acid)

Structure for NP0172632 ((2s,4r)-n-[(1s)-2-hydroxy-1-[(3r,4s,5r,6r)-3,4,5-trihydroxy-6-(methylsulfanyl)oxan-2-yl]propyl]-1-methyl-4-propylpyrrolidine-2-carboximidic acid)

3D Structure for NP0172632 ((2s,4r)-n-[(1s)-2-hydroxy-1-[(3r,4s,5r,6r)-3,4,5-trihydroxy-6-(methylsulfanyl)oxan-2-yl]propyl]-1-methyl-4-propylpyrrolidine-2-carboximidic acid)