NP-MRD: Showing NP-Card for (2s,3s,6r)-3-{[(3s)-3-carbamimidamido-1-hydroxy-5-(methylamino)pentylidene]amino}-6-(2-hydroxy-4-iminopyrimidin-1-yl)-3,6-dihydro-2h-pyran-2-carboxylic acid (NP0308725)

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Record Information

Version

2.0

Created at

2022-09-11 02:43:17 UTC

Updated at

2022-09-11 02:43:17 UTC

NP-MRD ID

NP0308725

Secondary Accession Numbers

None

Natural Product Identification

Common Name

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

Description

(2S,3S,6R)-3-{[(3S)-3-carbamimidamido-1-hydroxy-5-(methylamino)pentylidene]amino}-6-(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 hydroxypyrimidines. These are organic compounds containing a hydroxyl group attached 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-carbamimidamido-1-hydroxy-5-(methylamino)pentylidene]amino}-6-(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-carbamimidamido-1-hydroxy-5-(methylamino)pentylidene]amino}-6-(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


  Mrv1652309112204432D          

 30 31  0  0  1  0            999 V2000
   -1.2375   -5.8855    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125   -5.8855    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -6.6000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250   -6.6000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375   -7.3145    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.8250   -8.0289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375   -8.7434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0625   -8.7434    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250   -9.4579    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375  -10.1724    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.0625  -10.1724    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750  -10.8868    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0625  -11.6013    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.4750  -12.3158    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.3000  -12.3158    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7125  -13.0302    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3000  -13.7447    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7125  -14.4592    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750  -13.7447    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.0625  -13.0302    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375  -13.0302    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375  -11.6013    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250  -10.8868    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.0000  -10.8868    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125  -10.1724    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125  -11.6013    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0625   -7.3145    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750   -6.6000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3000   -6.6000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.0625   -5.8855    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  0  0  0  0
  6  7  1  0  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  2  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  6  0  0  0
 14 15  1  0  0  0  0
 15 16  2  0  0  0  0
 16 17  1  0  0  0  0
 17 18  2  0  0  0  0
 17 19  1  0  0  0  0
 19 20  2  0  0  0  0
 14 20  1  0  0  0  0
 20 21  1  0  0  0  0
 13 22  1  0  0  0  0
 22 23  1  0  0  0  0
 10 23  1  0  0  0  0
 23 24  1  6  0  0  0
 24 25  2  0  0  0  0
 24 26  1  0  0  0  0
  5 27  1  6  0  0  0
 27 28  1  0  0  0  0
 28 29  2  0  0  0  0
 28 30  1  0  0  0  0
M  END

     RDKit          3D

 56 57  0  0  0  0  0  0  0  0999 V2000
   -4.5201   -3.5946    1.0105 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1049   -3.0209    0.2458 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1024   -2.2366    0.4582 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5585   -2.1600    1.7616 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5859   -1.4845   -0.6242 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0024   -0.0911   -0.7437 C   0  0  1  0  0  0  0  0  0  0  0  0
   -4.5028   -0.0171   -0.8785 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0214    1.3872   -1.0184 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4834    1.3479   -1.1530 N   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1349    0.9357    0.0688 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5454    0.6547    0.4633 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0633    0.5991    0.6267 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5186    1.2683    1.7108 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3047   -0.0363   -0.1918 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.1044   -0.0540    0.0143 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.7494   -1.3617   -0.2783 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0086   -1.3651   -0.6761 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7846   -0.1168   -0.8362 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.1352   -0.2060   -0.3119 N   0  0  0  0  0  0  0  0  0  0  0  0
    6.2389   -0.1990   -1.0890 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.5170   -0.2834   -0.5698 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.7019   -0.3800    0.7959 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.8866   -0.4630    1.3398 N   0  0  0  0  0  0  0  0  0  0  0  0
    9.7443   -0.4590    0.7485 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.5864   -0.3851    1.5470 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.3525   -0.3015    1.0146 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2068   -0.3097    1.8290 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1396    1.0057   -0.2993 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8277    0.9920   -0.8238 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.1965    2.3209   -0.6994 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0260    2.4710   -1.1236 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8231    3.4254   -0.1371 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5635   -2.3846    1.9330 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1611   -1.8774    2.5496 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9271   -1.8645   -1.3414 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5093    0.3887   -1.6248 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7803   -0.5499   -1.8194 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0104   -0.5474   -0.0415 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8036    1.9892   -0.1048 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5949    1.9068   -1.8731 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7088    0.6947   -1.9399 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.6944    1.8123    0.5184 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.8990    0.1371   -0.1190 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4454    0.5621    0.8417 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9871    0.2058    1.3725 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8979    1.7085    0.4181 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6060    0.8409    2.6180 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3183    0.1366    1.1083 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1800   -2.3015   -0.1628 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4824   -2.2994   -0.8884 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8045    0.0776   -1.9479 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.0855   -0.1226   -2.1600 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.4073   -0.2786   -1.1914 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3054   -0.5748    2.7976 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9262    0.6332   -1.8682 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4981    3.8248    0.7449 H   0  0  0  0  0  0  0  0  0  0  0  0
 10  9  1  0
  9  8  1  0
  8  7  1  0
  7  6  1  0
  6 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 28  1  0
 28 29  1  0
 29 30  1  0
 30 32  1  0
 30 31  2  0
 18 19  1  0
 19 20  1  0
 20 21  2  0
 21 22  1  0
 22 23  2  0
 22 25  1  0
 25 26  2  0
 26 27  1  0
  6  5  1  0
  5  3  1  0
  3  4  1  0
  3  2  2  0
 29 15  1  0
 26 19  1  0
 10 42  1  0
 10 43  1  0
 10 44  1  0
  9 41  1  0
  8 39  1  0
  8 40  1  0
  7 37  1  0
  7 38  1  0
  6 36  1  6
 11 45  1  0
 11 46  1  0
 13 47  1  0
 15 48  1  1
 16 49  1  0
 17 50  1  0
 18 51  1  6
 29 55  1  6
 32 56  1  0
 20 52  1  0
 21 53  1  0
 23 24  1  0
 27 54  1  0
  5 35  1  0
  4 33  1  0
  4 34  1  0
  2  1  1  0
M  END


  Mrv1652309112204432D          

 30 31  0  0  1  0            999 V2000
   -1.2375   -5.8855    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125   -5.8855    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -6.6000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250   -6.6000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375   -7.3145    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.8250   -8.0289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375   -8.7434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0625   -8.7434    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250   -9.4579    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375  -10.1724    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.0625  -10.1724    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750  -10.8868    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0625  -11.6013    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.4750  -12.3158    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.3000  -12.3158    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7125  -13.0302    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3000  -13.7447    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7125  -14.4592    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750  -13.7447    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.0625  -13.0302    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375  -13.0302    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375  -11.6013    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250  -10.8868    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.0000  -10.8868    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125  -10.1724    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125  -11.6013    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0625   -7.3145    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750   -6.6000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3000   -6.6000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.0625   -5.8855    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  0  0  0  0
  6  7  1  0  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  2  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  6  0  0  0
 14 15  1  0  0  0  0
 15 16  2  0  0  0  0
 16 17  1  0  0  0  0
 17 18  2  0  0  0  0
 17 19  1  0  0  0  0
 19 20  2  0  0  0  0
 14 20  1  0  0  0  0
 20 21  1  0  0  0  0
 13 22  1  0  0  0  0
 22 23  1  0  0  0  0
 10 23  1  0  0  0  0
 23 24  1  6  0  0  0
 24 25  2  0  0  0  0
 24 26  1  0  0  0  0
  5 27  1  6  0  0  0
 27 28  1  0  0  0  0
 28 29  2  0  0  0  0
 28 30  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0308725

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C17H26N8O5/c1-21-6-4-9(22-16(19)20)8-12(26)23-10-2-3-13(30-14(10)15(27)28)25-7-5-11(18)24-17(25)29/h2-3,5,7,9-10,13-14,21H,4,6,8H2,1H3,(H,23,26)(H,27,28)(H2,18,24,29)(H4,19,20,22)/t9-,10-,13+,14-/m0/s1

> <INCHI_KEY>
VLSNCRSMCQBBPG-ZNIXKSQXSA-N

> <FORMULA>
C17H26N8O5

> <MOLECULAR_WEIGHT>
422.446

> <EXACT_MASS>
422.202615969

> <JCHEM_ACCEPTOR_COUNT>
13

> <JCHEM_ATOM_COUNT>
56

> <JCHEM_AVERAGE_POLARIZABILITY>
42.11218900173429

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
8

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <JCHEM_LOGP>
-5.506078550954129

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
5.23695988663256

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.522618582596136

> <JCHEM_PKA_STRONGEST_BASIC>
12.207719876464187

> <JCHEM_POLAR_SURFACE_AREA>
212.73000000000002

> <JCHEM_REFRACTIVITY>
127.8375

> <JCHEM_ROTATABLE_BOND_COUNT>
9

> <JCHEM_RULE_OF_FIVE>
0

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

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 11-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   11-SEP-22         0                                  
HETATM    1  C   UNK     0      -2.310 -10.986   0.000  0.00  0.00           C+0
HETATM    2  N   UNK     0      -0.770 -10.986   0.000  0.00  0.00           N+0
HETATM    3  C   UNK     0       0.000 -12.320   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.540 -12.320   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.310 -13.654   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.540 -14.987   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       2.310 -16.321   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       3.850 -16.321   0.000  0.00  0.00           O+0
HETATM    9  N   UNK     0       1.540 -17.655   0.000  0.00  0.00           N+0
HETATM   10  C   UNK     0       2.310 -18.988   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       3.850 -18.988   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       4.620 -20.322   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       3.850 -21.656   0.000  0.00  0.00           C+0
HETATM   14  N   UNK     0       4.620 -22.989   0.000  0.00  0.00           N+0
HETATM   15  C   UNK     0       6.160 -22.989   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       6.930 -24.323   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       6.160 -25.657   0.000  0.00  0.00           C+0
HETATM   18  N   UNK     0       6.930 -26.990   0.000  0.00  0.00           N+0
HETATM   19  N   UNK     0       4.620 -25.657   0.000  0.00  0.00           N+0
HETATM   20  C   UNK     0       3.850 -24.323   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0       2.310 -24.323   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0       2.310 -21.656   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0       1.540 -20.322   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       0.000 -20.322   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0      -0.770 -18.988   0.000  0.00  0.00           O+0
HETATM   26  O   UNK     0      -0.770 -21.656   0.000  0.00  0.00           O+0
HETATM   27  N   UNK     0       3.850 -13.654   0.000  0.00  0.00           N+0
HETATM   28  C   UNK     0       4.620 -12.320   0.000  0.00  0.00           C+0
HETATM   29  N   UNK     0       6.160 -12.320   0.000  0.00  0.00           N+0
HETATM   30  N   UNK     0       3.850 -10.986   0.000  0.00  0.00           N+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6   27                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10                                                       
CONECT   10    9   11   23                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14   22                                                  
CONECT   14   13   15   20                                                  
CONECT   15   14   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16   18   19                                                  
CONECT   18   17                                                            
CONECT   19   17   20                                                       
CONECT   20   19   14   21                                                  
CONECT   21   20                                                            
CONECT   22   13   23                                                       
CONECT   23   22   10   24                                                  
CONECT   24   23   25   26                                                  
CONECT   25   24                                                            
CONECT   26   24                                                            
CONECT   27    5   28                                                       
CONECT   28   27   29   30                                                  
CONECT   29   28                                                            
CONECT   30   28                                                            
MASTER        0    0    0    0    0    0    0    0   30    0   62    0
END

View in JSmol

Synonyms

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

Chemical Formula

C₁₇H₂₆N₈O₅

Average Mass

422.4460 Da

Monoisotopic Mass

422.20262 Da

IUPAC Name

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

CAS Registry Number

Not Available

SMILES

CNCC[C@@H](CC(O)=N[C@H]1C=C[C@@H](O[C@@H]1C(O)=O)N1C=CC(=N)N=C1O)NC(N)=N

InChI Identifier

InChI=1S/C17H26N8O5/c1-21-6-4-9(22-16(19)20)8-12(26)23-10-2-3-13(30-14(10)15(27)28)25-7-5-11(18)24-17(25)29/h2-3,5,7,9-10,13-14,21H,4,6,8H2,1H3,(H,23,26)(H,27,28)(H2,18,24,29)(H4,19,20,22)/t9-,10-,13+,14-/m0/s1

InChI Key

VLSNCRSMCQBBPG-ZNIXKSQXSA-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 hydroxypyrimidines. These are organic compounds containing a hydroxyl group attached 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

Hydroxypyrimidines

Alternative Parents

Substituents

Hydroxypyrimidine
Hydropyrimidine
Pyran
Heteroaromatic compound
Amino acid
Amino acid or derivatives
Guanidine
Carboximidic acid
Carboximidic acid derivative
Carboxylic acid derivative
Carboxylic acid
Secondary aliphatic amine
Monocarboxylic acid or derivatives
Secondary amine
Carboximidamide
Propargyl-type 1,3-dipolar organic compound
Organic 1,3-dipolar compound
Azacycle
Oxacycle
Organopnictogen compound
Organonitrogen compound
Organooxygen compound
Organic oxygen compound
Carbonyl group
Organic oxide
Hydrocarbon derivative
Organic nitrogen compound
Imine
Amine
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	-5.5	ChemAxon
pKa (Strongest Acidic)	2.52	ChemAxon
pKa (Strongest Basic)	12.21	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	13	ChemAxon
Hydrogen Donor Count	8	ChemAxon
Polar Surface Area	212.73 Å²	ChemAxon
Rotatable Bond Count	9	ChemAxon
Refractivity	127.84 m³·mol⁻¹	ChemAxon
Polarizability	42.11 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

163018417

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-carbamimidamido-1-hydroxy-5-(methylamino)pentylidene]amino}-6-(2-hydroxy-4-iminopyrimidin-1-yl)-3,6-dihydro-2h-pyran-2-carboxylic acid (NP0308725)

MOL for NP0308725 ((2s,3s,6r)-3-{[(3s)-3-carbamimidamido-1-hydroxy-5-(methylamino)pentylidene]amino}-6-(2-hydroxy-4-iminopyrimidin-1-yl)-3,6-dihydro-2h-pyran-2-carboxylic acid)

3D MOL for NP0308725 ((2s,3s,6r)-3-{[(3s)-3-carbamimidamido-1-hydroxy-5-(methylamino)pentylidene]amino}-6-(2-hydroxy-4-iminopyrimidin-1-yl)-3,6-dihydro-2h-pyran-2-carboxylic acid)

3D SDF for NP0308725 ((2s,3s,6r)-3-{[(3s)-3-carbamimidamido-1-hydroxy-5-(methylamino)pentylidene]amino}-6-(2-hydroxy-4-iminopyrimidin-1-yl)-3,6-dihydro-2h-pyran-2-carboxylic acid)

3D-SDF for NP0308725 ((2s,3s,6r)-3-{[(3s)-3-carbamimidamido-1-hydroxy-5-(methylamino)pentylidene]amino}-6-(2-hydroxy-4-iminopyrimidin-1-yl)-3,6-dihydro-2h-pyran-2-carboxylic acid)

PDB for NP0308725 ((2s,3s,6r)-3-{[(3s)-3-carbamimidamido-1-hydroxy-5-(methylamino)pentylidene]amino}-6-(2-hydroxy-4-iminopyrimidin-1-yl)-3,6-dihydro-2h-pyran-2-carboxylic acid)

3D PDB for NP0308725 ((2s,3s,6r)-3-{[(3s)-3-carbamimidamido-1-hydroxy-5-(methylamino)pentylidene]amino}-6-(2-hydroxy-4-iminopyrimidin-1-yl)-3,6-dihydro-2h-pyran-2-carboxylic acid)

SMILES for NP0308725 ((2s,3s,6r)-3-{[(3s)-3-carbamimidamido-1-hydroxy-5-(methylamino)pentylidene]amino}-6-(2-hydroxy-4-iminopyrimidin-1-yl)-3,6-dihydro-2h-pyran-2-carboxylic acid)

INCHI for NP0308725 ((2s,3s,6r)-3-{[(3s)-3-carbamimidamido-1-hydroxy-5-(methylamino)pentylidene]amino}-6-(2-hydroxy-4-iminopyrimidin-1-yl)-3,6-dihydro-2h-pyran-2-carboxylic acid)

Structure for NP0308725 ((2s,3s,6r)-3-{[(3s)-3-carbamimidamido-1-hydroxy-5-(methylamino)pentylidene]amino}-6-(2-hydroxy-4-iminopyrimidin-1-yl)-3,6-dihydro-2h-pyran-2-carboxylic acid)

3D Structure for NP0308725 ((2s,3s,6r)-3-{[(3s)-3-carbamimidamido-1-hydroxy-5-(methylamino)pentylidene]amino}-6-(2-hydroxy-4-iminopyrimidin-1-yl)-3,6-dihydro-2h-pyran-2-carboxylic acid)