NP-MRD: Showing NP-Card for (2s,3s,6r)-3-{[(3s)-3-amino-1-hydroxy-5-(n-methylcarbamimidamido)pentylidene]amino}-6-(5-fluoro-2-hydroxy-4-iminopyrimidin-1-yl)-3,6-dihydro-2h-pyran-2-carboxylic acid (NP0149196)

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Record Information

Version

2.0

Created at

2022-09-02 05:02:50 UTC

Updated at

2022-09-02 05:02:50 UTC

NP-MRD ID

NP0149196

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(2s,3s,6r)-3-{[(3s)-3-amino-1-hydroxy-5-(n-methylcarbamimidamido)pentylidene]amino}-6-(5-fluoro-2-hydroxy-4-iminopyrimidin-1-yl)-3,6-dihydro-2h-pyran-2-carboxylic acid

Description

(2S,3S,6R)-3-{[(3S)-3-amino-1-hydroxy-5-(N-methylcarbamimidamido)pentylidene]amino}-6-(5-fluoro-2-hydroxy-4-imino-1,4-dihydropyrimidin-1-yl)-3,6-dihydro-2H-pyran-2-carboxylic acid belongs to the class of organic compounds known as halopyrimidines. These are aromatic compounds containing a halogen atom linked to a pyrimidine ring. Pyrimidine is a 6-membered ring consisting of four carbon atoms and two nitrogen centers at the 1- and 3- ring positions. (2s,3s,6r)-3-{[(3s)-3-amino-1-hydroxy-5-(n-methylcarbamimidamido)pentylidene]amino}-6-(5-fluoro-2-hydroxy-4-iminopyrimidin-1-yl)-3,6-dihydro-2h-pyran-2-carboxylic acid is found in Streptomyces griseochromogenes. Based on a literature review very few articles have been published on (2S,3S,6R)-3-{[(3S)-3-amino-1-hydroxy-5-(N-methylcarbamimidamido)pentylidene]amino}-6-(5-fluoro-2-hydroxy-4-imino-1,4-dihydropyrimidin-1-yl)-3,6-dihydro-2H-pyran-2-carboxylic acid.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309022207022D          

 31 32  0  0  1  0            999 V2000
    1.4289   -4.1250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -4.9500    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -5.3625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -5.3625    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.7145   -6.1875    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -5.3625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -6.1875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8579   -4.9500    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724   -5.3625    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.5724   -6.1875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2868   -6.6000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0013   -6.1875    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -5.7158   -6.6000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7158   -7.4250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4302   -7.8375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4302   -8.6625    0.0000 F   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1447   -7.4250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.8592   -7.8375    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1447   -6.6000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4302   -6.1875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4302   -5.3625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0013   -5.3625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2868   -4.9500    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -4.2868   -4.1250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724   -3.7125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0013   -3.7125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -5.3625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -4.9500    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -6.1875    0.0000 N   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  6  0  0  0
  5  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  4  0  0  0
  8 10  2  0  0  0  0
 11 10  1  1  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  6  0  0  0
 15 16  1  0  0  0  0
 16 17  2  0  0  0  0
 17 18  1  0  0  0  0
 17 19  1  0  0  0  0
 19 20  2  0  0  0  0
 19 21  1  0  0  0  0
 21 22  2  0  0  0  0
 15 22  1  0  0  0  0
 22 23  1  0  0  0  0
 14 24  1  0  0  0  0
 24 25  1  0  0  0  0
 11 25  1  0  0  0  0
 25 26  1  6  0  0  0
 26 27  2  0  0  0  0
 26 28  1  0  0  0  0
  2 29  1  0  0  0  0
 29 30  2  0  0  0  0
 29 31  1  0  0  0  0
M  END

     RDKit          3D

 56 57  0  0  0  0  0  0  0  0999 V2000
   -7.3041    2.7207   -0.2335 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7657    1.9285   -0.6213 N   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8287    0.7783   -0.0499 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.6335    0.6075    1.1027 N   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0907   -0.3072   -0.5814 N   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7822   -1.3240   -1.3280 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6633   -0.3691   -0.3629 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9114   -0.1640   -1.6622 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4346   -0.2390   -1.4319 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.0287   -1.5261   -0.8860 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9265    0.8265   -0.4900 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4400    0.5867   -0.3900 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2595    0.6754   -1.5788 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0419    0.3290    0.7464 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.3832    0.0643    1.1308 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.8907   -1.2504    0.6781 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1288   -1.4042    0.2559 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0478   -0.2501    0.2255 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.4114   -0.6168    0.5295 N   0  0  0  0  0  0  0  0  0  0  0  0
    6.1002   -0.1267    1.5652 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.4163   -0.5123    1.8195 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.1200   -0.0283    2.8547 F   0  0  0  0  0  0  0  0  0  0  0  0
    8.0157   -1.4215    0.9783 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.2304   -1.8206    1.1567 N   0  0  0  0  0  0  0  0  0  0  0  0
    9.7662   -1.4402    1.9614 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.3071   -1.8972   -0.0501 N   0  0  0  0  0  0  0  0  0  0  0  0
    6.0228   -1.5033   -0.2752 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4029   -2.0770   -1.3805 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6007    0.8068    1.0166 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3012    1.1136    0.5451 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.9163    2.4910    0.9175 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7779    2.8808    0.5510 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7088    3.3606    1.6274 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.5989    1.2926    1.9064 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.2914   -0.2016    1.2022 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.6828   -0.9456   -1.8232 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1226   -1.7258   -2.1315 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0432   -2.1529   -0.6107 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3643   -1.3648    0.0385 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3979    0.3968    0.3881 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1512    0.8877   -1.9803 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2640   -0.8776   -2.4150 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8947   -0.0897   -2.4032 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6050   -1.4367    0.0451 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7701   -2.2465   -0.9718 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1105    1.8546   -0.8924 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4081    0.6734    0.4945 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5219   -0.1699   -2.0808 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4055    0.1142    2.2612 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2005   -2.0906    0.7070 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4737   -2.3700   -0.0676 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0034    0.1461   -0.8319 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.6252    0.5825    2.2171 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7880   -1.5060   -1.9261 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3265    0.9563   -0.5524 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3196    3.9812    1.0862 H   0  0  0  0  0  0  0  0  0  0  0  0
  6  5  1  0
  5  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
  9 11  1  0
 11 12  1  0
 12 13  1  0
 12 14  2  0
 14 15  1  0
 15 16  1  0
 16 17  2  0
 17 18  1  0
 18 29  1  0
 29 30  1  0
 30 31  1  0
 31 33  1  0
 31 32  2  0
 18 19  1  0
 19 20  1  0
 20 21  2  0
 21 22  1  0
 21 23  1  0
 23 24  2  0
 23 26  1  0
 26 27  2  0
 27 28  1  0
  5  3  1  0
  3  4  1  0
  3  2  2  0
 30 15  1  0
 27 19  1  0
  6 36  1  0
  6 37  1  0
  6 38  1  0
  7 39  1  0
  7 40  1  0
  8 41  1  0
  8 42  1  0
  9 43  1  6
 10 44  1  0
 10 45  1  0
 11 46  1  0
 11 47  1  0
 13 48  1  0
 15 49  1  1
 16 50  1  0
 17 51  1  0
 18 52  1  6
 30 55  1  6
 33 56  1  0
 20 53  1  0
 24 25  1  0
 28 54  1  0
  4 34  1  0
  4 35  1  0
  2  1  1  0
M  END


  Mrv1652309022207022D          

 31 32  0  0  1  0            999 V2000
    1.4289   -4.1250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -4.9500    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -5.3625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -5.3625    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.7145   -6.1875    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -5.3625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -6.1875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8579   -4.9500    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724   -5.3625    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.5724   -6.1875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2868   -6.6000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0013   -6.1875    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -5.7158   -6.6000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7158   -7.4250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4302   -7.8375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4302   -8.6625    0.0000 F   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1447   -7.4250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.8592   -7.8375    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1447   -6.6000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4302   -6.1875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4302   -5.3625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0013   -5.3625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2868   -4.9500    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -4.2868   -4.1250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724   -3.7125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0013   -3.7125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -5.3625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -4.9500    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -6.1875    0.0000 N   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  6  0  0  0
  5  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  4  0  0  0
  8 10  2  0  0  0  0
 11 10  1  1  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  6  0  0  0
 15 16  1  0  0  0  0
 16 17  2  0  0  0  0
 17 18  1  0  0  0  0
 17 19  1  0  0  0  0
 19 20  2  0  0  0  0
 19 21  1  0  0  0  0
 21 22  2  0  0  0  0
 15 22  1  0  0  0  0
 22 23  1  0  0  0  0
 14 24  1  0  0  0  0
 24 25  1  0  0  0  0
 11 25  1  0  0  0  0
 25 26  1  6  0  0  0
 26 27  2  0  0  0  0
 26 28  1  0  0  0  0
  2 29  1  0  0  0  0
 29 30  2  0  0  0  0
 29 31  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0149196

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CN(CC[C@H](N)CC(O)=N[C@H]1C=C[C@@H](O[C@@H]1C(O)=O)N1C=C(F)C(=N)N=C1O)C(N)=N

> <INCHI_IDENTIFIER>
InChI=1S/C17H25FN8O5/c1-25(16(21)22)5-4-8(19)6-11(27)23-10-2-3-12(31-13(10)15(28)29)26-7-9(18)14(20)24-17(26)30/h2-3,7-8,10,12-13H,4-6,19H2,1H3,(H3,21,22)(H,23,27)(H,28,29)(H2,20,24,30)/t8-,10-,12+,13-/m0/s1

> <INCHI_KEY>
GWLMNHVGZNODLR-ZDAZMGEQSA-N

> <FORMULA>
C17H25FN8O5

> <MOLECULAR_WEIGHT>
440.436

> <EXACT_MASS>
440.1931941

> <JCHEM_ACCEPTOR_COUNT>
13

> <JCHEM_ATOM_COUNT>
56

> <JCHEM_AVERAGE_POLARIZABILITY>
42.80729422253354

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
7

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S,3S,6R)-3-{[(3S)-3-amino-1-hydroxy-5-(N-methylcarbamimidamido)pentylidene]amino}-6-(5-fluoro-2-hydroxy-4-imino-1,4-dihydropyrimidin-1-yl)-3,6-dihydro-2H-pyran-2-carboxylic acid

> <ALOGPS_LOGP>
-1.92

> <JCHEM_LOGP>
-5.199480886242263

> <ALOGPS_LOGS>
-3.68

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
4.899172032476093

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.3901515109270752

> <JCHEM_PKA_STRONGEST_BASIC>
12.225011700562943

> <JCHEM_POLAR_SURFACE_AREA>
217.92999999999998

> <JCHEM_REFRACTIVITY>
128.56050000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
9.14e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2S,3S,6R)-3-{[(3S)-3-amino-1-hydroxy-5-(N-methylcarbamimidamido)pentylidene]amino}-6-(5-fluoro-2-hydroxy-4-iminopyrimidin-1-yl)-3,6-dihydro-2H-pyran-2-carboxylic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 02-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   02-SEP-22         0                                  
HETATM    1  C   UNK     0       2.667  -7.700   0.000  0.00  0.00           C+0
HETATM    2  N   UNK     0       2.667  -9.240   0.000  0.00  0.00           N+0
HETATM    3  C   UNK     0       1.334 -10.010   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.000  -9.240   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -1.334 -10.010   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0      -1.334 -11.550   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0      -2.667  -9.240   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -4.001 -10.010   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0      -4.001 -11.550   0.000  0.00  0.00           O+0
HETATM   10  N   UNK     0      -5.335  -9.240   0.000  0.00  0.00           N+0
HETATM   11  C   UNK     0      -6.668 -10.010   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -6.668 -11.550   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -8.002 -12.320   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -9.336 -11.550   0.000  0.00  0.00           C+0
HETATM   15  N   UNK     0     -10.669 -12.320   0.000  0.00  0.00           N+0
HETATM   16  C   UNK     0     -10.669 -13.860   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0     -12.003 -14.630   0.000  0.00  0.00           C+0
HETATM   18  F   UNK     0     -12.003 -16.170   0.000  0.00  0.00           F+0
HETATM   19  C   UNK     0     -13.337 -13.860   0.000  0.00  0.00           C+0
HETATM   20  N   UNK     0     -14.670 -14.630   0.000  0.00  0.00           N+0
HETATM   21  N   UNK     0     -13.337 -12.320   0.000  0.00  0.00           N+0
HETATM   22  C   UNK     0     -12.003 -11.550   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0     -12.003 -10.010   0.000  0.00  0.00           O+0
HETATM   24  O   UNK     0      -9.336 -10.010   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0      -8.002  -9.240   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      -8.002  -7.700   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0      -6.668  -6.930   0.000  0.00  0.00           O+0
HETATM   28  O   UNK     0      -9.336  -6.930   0.000  0.00  0.00           O+0
HETATM   29  C   UNK     0       4.001 -10.010   0.000  0.00  0.00           C+0
HETATM   30  N   UNK     0       5.335  -9.240   0.000  0.00  0.00           N+0
HETATM   31  N   UNK     0       4.001 -11.550   0.000  0.00  0.00           N+0
CONECT    1    2                                                            
CONECT    2    1    3   29                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5    8                                                       
CONECT    8    7    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8   11                                                       
CONECT   11   10   12   25                                                  
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15   24                                                  
CONECT   15   14   16   22                                                  
CONECT   16   15   17                                                       
CONECT   17   16   18   19                                                  
CONECT   18   17                                                            
CONECT   19   17   20   21                                                  
CONECT   20   19                                                            
CONECT   21   19   22                                                       
CONECT   22   21   15   23                                                  
CONECT   23   22                                                            
CONECT   24   14   25                                                       
CONECT   25   24   11   26                                                  
CONECT   26   25   27   28                                                  
CONECT   27   26                                                            
CONECT   28   26                                                            
CONECT   29    2   30   31                                                  
CONECT   30   29                                                            
CONECT   31   29                                                            
MASTER        0    0    0    0    0    0    0    0   31    0   64    0
END

View in JSmol

Synonyms

Value	Source
(2S,3S,6R)-3-{[(3S)-3-amino-1-hydroxy-5-(N-methylcarbamimidamido)pentylidene]amino}-6-(5-fluoro-2-hydroxy-4-imino-1,4-dihydropyrimidin-1-yl)-3,6-dihydro-2H-pyran-2-carboxylate	Generator

Chemical Formula

C₁₇H₂₅FN₈O₅

Average Mass

440.4360 Da

Monoisotopic Mass

440.19319 Da

IUPAC Name

(2S,3S,6R)-3-{[(3S)-3-amino-1-hydroxy-5-(N-methylcarbamimidamido)pentylidene]amino}-6-(5-fluoro-2-hydroxy-4-imino-1,4-dihydropyrimidin-1-yl)-3,6-dihydro-2H-pyran-2-carboxylic acid

Traditional Name

(2S,3S,6R)-3-{[(3S)-3-amino-1-hydroxy-5-(N-methylcarbamimidamido)pentylidene]amino}-6-(5-fluoro-2-hydroxy-4-iminopyrimidin-1-yl)-3,6-dihydro-2H-pyran-2-carboxylic acid

CAS Registry Number

Not Available

SMILES

CN(CC[C@H](N)CC(O)=N[C@H]1C=C[C@@H](O[C@@H]1C(O)=O)N1C=C(F)C(=N)N=C1O)C(N)=N

InChI Identifier

InChI=1S/C17H25FN8O5/c1-25(16(21)22)5-4-8(19)6-11(27)23-10-2-3-12(31-13(10)15(28)29)26-7-9(18)14(20)24-17(26)30/h2-3,7-8,10,12-13H,4-6,19H2,1H3,(H3,21,22)(H,23,27)(H,28,29)(H2,20,24,30)/t8-,10-,12+,13-/m0/s1

InChI Key

GWLMNHVGZNODLR-ZDAZMGEQSA-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 griseochromogenes	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as halopyrimidines. These are aromatic compounds containing a halogen atom linked to a pyrimidine ring. Pyrimidine is a 6-membered ring consisting of four carbon atoms and two nitrogen centers at the 1- and 3- ring positions.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Diazines

Sub Class

Pyrimidines and pyrimidine derivatives

Direct Parent

Halopyrimidines

Alternative Parents

Substituents

Hydroxypyrimidine
Halopyrimidine
Aryl fluoride
Aryl halide
Hydropyrimidine
Pyran
Heteroaromatic compound
Amino acid or derivatives
Guanidine
Amino acid
Carboximidic acid
Carboximidic acid derivative
Carboxylic acid derivative
Carboxylic acid
Oxacycle
Monocarboxylic acid or derivatives
Azacycle
Carboximidamide
Propargyl-type 1,3-dipolar organic compound
Organic 1,3-dipolar compound
Primary aliphatic amine
Imine
Organopnictogen compound
Hydrocarbon derivative
Organic oxide
Carbonyl group
Organohalogen compound
Organofluoride
Organonitrogen compound
Organooxygen compound
Primary amine
Amine
Organic nitrogen compound
Organic oxygen compound
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic 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	-1.9	ALOGPS
logP	-5.2	ChemAxon
logS	-3.7	ALOGPS
pKa (Strongest Acidic)	3.39	ChemAxon
pKa (Strongest Basic)	12.23	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	13	ChemAxon
Hydrogen Donor Count	7	ChemAxon
Polar Surface Area	217.93 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	128.56 m³·mol⁻¹	ChemAxon
Polarizability	42.81 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	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

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

13556539

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for (2s,3s,6r)-3-{[(3s)-3-amino-1-hydroxy-5-(n-methylcarbamimidamido)pentylidene]amino}-6-(5-fluoro-2-hydroxy-4-iminopyrimidin-1-yl)-3,6-dihydro-2h-pyran-2-carboxylic acid (NP0149196)

MOL for NP0149196 ((2s,3s,6r)-3-{[(3s)-3-amino-1-hydroxy-5-(n-methylcarbamimidamido)pentylidene]amino}-6-(5-fluoro-2-hydroxy-4-iminopyrimidin-1-yl)-3,6-dihydro-2h-pyran-2-carboxylic acid)

3D MOL for NP0149196 ((2s,3s,6r)-3-{[(3s)-3-amino-1-hydroxy-5-(n-methylcarbamimidamido)pentylidene]amino}-6-(5-fluoro-2-hydroxy-4-iminopyrimidin-1-yl)-3,6-dihydro-2h-pyran-2-carboxylic acid)

3D SDF for NP0149196 ((2s,3s,6r)-3-{[(3s)-3-amino-1-hydroxy-5-(n-methylcarbamimidamido)pentylidene]amino}-6-(5-fluoro-2-hydroxy-4-iminopyrimidin-1-yl)-3,6-dihydro-2h-pyran-2-carboxylic acid)

3D-SDF for NP0149196 ((2s,3s,6r)-3-{[(3s)-3-amino-1-hydroxy-5-(n-methylcarbamimidamido)pentylidene]amino}-6-(5-fluoro-2-hydroxy-4-iminopyrimidin-1-yl)-3,6-dihydro-2h-pyran-2-carboxylic acid)

PDB for NP0149196 ((2s,3s,6r)-3-{[(3s)-3-amino-1-hydroxy-5-(n-methylcarbamimidamido)pentylidene]amino}-6-(5-fluoro-2-hydroxy-4-iminopyrimidin-1-yl)-3,6-dihydro-2h-pyran-2-carboxylic acid)

3D PDB for NP0149196 ((2s,3s,6r)-3-{[(3s)-3-amino-1-hydroxy-5-(n-methylcarbamimidamido)pentylidene]amino}-6-(5-fluoro-2-hydroxy-4-iminopyrimidin-1-yl)-3,6-dihydro-2h-pyran-2-carboxylic acid)

SMILES for NP0149196 ((2s,3s,6r)-3-{[(3s)-3-amino-1-hydroxy-5-(n-methylcarbamimidamido)pentylidene]amino}-6-(5-fluoro-2-hydroxy-4-iminopyrimidin-1-yl)-3,6-dihydro-2h-pyran-2-carboxylic acid)

INCHI for NP0149196 ((2s,3s,6r)-3-{[(3s)-3-amino-1-hydroxy-5-(n-methylcarbamimidamido)pentylidene]amino}-6-(5-fluoro-2-hydroxy-4-iminopyrimidin-1-yl)-3,6-dihydro-2h-pyran-2-carboxylic acid)

Structure for NP0149196 ((2s,3s,6r)-3-{[(3s)-3-amino-1-hydroxy-5-(n-methylcarbamimidamido)pentylidene]amino}-6-(5-fluoro-2-hydroxy-4-iminopyrimidin-1-yl)-3,6-dihydro-2h-pyran-2-carboxylic acid)

3D Structure for NP0149196 ((2s,3s,6r)-3-{[(3s)-3-amino-1-hydroxy-5-(n-methylcarbamimidamido)pentylidene]amino}-6-(5-fluoro-2-hydroxy-4-iminopyrimidin-1-yl)-3,6-dihydro-2h-pyran-2-carboxylic acid)