NP-MRD: Showing NP-Card for Agrocin 108 (NP0017486)

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Record Information

Version

2.0

Created at

2021-01-06 02:11:17 UTC

Updated at

2021-07-15 17:25:38 UTC

NP-MRD ID

NP0017486

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Agrocin 108

Provided By

NPAtlas

Description

Agrocin 108 belongs to the class of organic compounds known as pyrimidine ribonucleoside monophosphates. These are pyrimidine ribobucleotides with monophosphate group linked to the ribose moiety. Agrocin 108 is found in Rhizobium. Agrocin 108 was first documented in 2018 (PMID: 29348528). Based on a literature review very few articles have been published on Agrocin 108.

Structure

MOL 3D MOL SDF 3D SDF PDB SMILES InChI


  Mrv1652306242104243D          

 70 73  0  0  0  0            999 V2000
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M  END

     RDKit          3D

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M  END


  Mrv1652306242104243D          

 70 73  0  0  0  0            999 V2000
   -3.9271    7.7218    0.4263 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6024    6.3398    0.4939 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4618    5.3539    0.0455 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0869    4.0151    0.1384 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9056    3.6443    0.6547 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5958    2.2491    0.7147 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.3963    1.9766    1.3404 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1737    0.6425    1.1170 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.3037    0.2798    1.2236 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.4716   -1.0952    0.9861 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0842   -1.5410    1.0932 P   0  0  1  0  0  5  0  0  0  0  0  0
    2.7135   -1.0287    2.3547 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1370   -3.2485    1.0324 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8860   -0.9786   -0.3053 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2797   -0.7443   -0.2469 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2332   -1.6296   -0.4649 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9454   -2.9625   -0.7929 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.5509   -0.9963   -0.3104 C   0  0  1  0  0  0  0  0  0  0  0  0
    7.5025   -1.8550    0.3716 N   0  0  1  0  0  0  0  0  0  0  0  0
    7.0387   -0.6711   -1.7221 C   0  0  1  0  0  0  0  0  0  0  0  0
    8.2519   -0.0272   -1.6131 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.2892    0.2732    0.4411 C   0  0  1  0  0  0  0  0  0  0  0  0
    7.1312    1.3148    0.0673 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.8778    0.5411    0.0720 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3090    1.6412    0.0384 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7139    0.3154   -0.2563 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.7223   -0.6076   -0.1219 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5539   -1.7274   -0.9306 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.6180   -1.7852   -1.7994 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3551   -2.9429   -1.7340 C   0  0  2  0  0  0  0  0  0  0  0  0
   -4.9231   -3.2189   -0.3574 C   0  0  1  0  0  0  0  0  0  0  0  0
   -5.5478   -4.4786   -0.4282 O   0  0  0  0  0  0  0  0  0  0  0  0
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   -3.7328   -4.4936    1.2087 O   0  0  0  0  0  0  0  0  0  0  0  0
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    0.9115    0.8807    0.5130 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6206    0.4912    2.2596 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3608   -3.5614    1.9387 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9793   -3.6966   -0.0999 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.4041   -2.8162   -0.0531 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.4569   -1.5237    0.0803 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.1168   -1.6340   -2.2594 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.2481   -0.0179   -2.1697 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.2087    0.8352   -2.1307 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.3367    0.0713    1.5360 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.8008    1.5346    0.7559 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9332    0.0309   -0.9770 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6251   -1.6268   -1.5171 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8474   -3.8375   -2.1299 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2490   -2.7892   -2.4032 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6612   -2.4578   -0.0613 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3267   -4.4097   -1.0355 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9446   -2.4623    1.4180 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3492   -4.4808    1.9833 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7490   -2.7096    0.8004 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4271   -4.8143   -0.4552 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6439    2.2534   -1.2192 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4007    1.6025   -2.3052 H   0  0  0  0  0  0  0  0  0  0  0  0
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  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
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 11 12  2  0  0  0  0
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 22 24  1  0  0  0  0
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  8 26  1  0  0  0  0
 26 27  1  0  0  0  0
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 37 38  1  0  0  0  0
  5 39  1  0  0  0  0
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 41  2  2  0  0  0  0
 37  6  1  0  0  0  0
 24 15  1  0  0  0  0
 35 28  1  0  0  0  0
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 37 69  1  6  0  0  0
 38 70  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0017486

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H]OC1=C(O[P@](=O)(O[H])OC([H])([H])[C@@]2([H])O[C@@]([H])(N3C([H])=C([H])C(=NC3=O)N([H])[H])[C@]([H])(O[H])[C@]2([H])O[C@]2([H])OC([H])([H])[C@@]([H])(O[H])[C@@]([H])(O[H])[C@@]2([H])O[H])C(=O)[C@]([H])(O[H])[C@]1(N([H])[H])C([H])([H])O[H]

> <INCHI_IDENTIFIER>
InChI=1S/C20H29N4O16P/c21-8-1-2-24(19(33)23-8)17-12(30)13(39-18-10(28)9(27)6(26)3-36-18)7(38-17)4-37-41(34,35)40-14-11(29)15(31)20(22,5-25)16(14)32/h1-2,6-7,9-10,12-13,15,17-18,25-28,30-32H,3-5,22H2,(H,34,35)(H2,21,23,33)/t6-,7-,9-,10-,12-,13-,15+,17-,18+,20-/m1/s1

> <INCHI_KEY>
YUMCOBIDABFYCR-HHLCLMOPSA-N

> <FORMULA>
C20H29N4O16P

> <MOLECULAR_WEIGHT>
612.438

> <EXACT_MASS>
612.131617868

> <JCHEM_ACCEPTOR_COUNT>
17

> <JCHEM_ATOM_COUNT>
70

> <JCHEM_AVERAGE_POLARIZABILITY>
54.99906903930507

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
10

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
{[(3R,4R)-3-amino-2,4-dihydroxy-3-(hydroxymethyl)-5-oxocyclopent-1-en-1-yl]oxy}({[(2R,3S,4R,5R)-5-(4-amino-2-oxo-1,2-dihydropyrimidin-1-yl)-4-hydroxy-3-{[(2S,3R,4R,5R)-3,4,5-trihydroxyoxan-2-yl]oxy}oxolan-2-yl]methoxy})phosphinic acid

> <ALOGPS_LOGP>
-2.20

> <JCHEM_LOGP>
-7.564190366457088

> <ALOGPS_LOGS>
-1.28

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
4.02354278649915

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.2245037604268685

> <JCHEM_PKA_STRONGEST_BASIC>
8.566146811657248

> <JCHEM_POLAR_SURFACE_AREA>
326.84

> <JCHEM_REFRACTIVITY>
127.228

> <JCHEM_ROTATABLE_BOND_COUNT>
9

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
3.22e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
[(3R,4R)-3-amino-2,4-dihydroxy-3-(hydroxymethyl)-5-oxocyclopent-1-en-1-yl]oxy([(2R,3S,4R,5R)-5-(4-amino-2-oxopyrimidin-1-yl)-4-hydroxy-3-{[(2S,3R,4R,5R)-3,4,5-trihydroxyoxan-2-yl]oxy}oxolan-2-yl]methoxy)phosphinic acid

> <JCHEM_VEBER_RULE>
0

$$$$

     RDKit          3D

 70 73  0  0  0  0  0  0  0  0999 V2000
   -3.9271    7.7218    0.4263 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6024    6.3398    0.4939 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4618    5.3539    0.0455 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0869    4.0151    0.1384 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9056    3.6443    0.6547 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5958    2.2491    0.7147 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.3963    1.9766    1.3404 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1737    0.6425    1.1170 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.3037    0.2798    1.2236 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4716   -1.0952    0.9861 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0842   -1.5410    1.0932 P   0  0  1  0  0  5  0  0  0  0  0  0
    2.7135   -1.0287    2.3547 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1370   -3.2485    1.0324 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8860   -0.9786   -0.3053 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2797   -0.7443   -0.2469 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2332   -1.6296   -0.4649 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9454   -2.9625   -0.7929 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.5509   -0.9963   -0.3104 C   0  0  1  0  0  0  0  0  0  0  0  0
    7.5025   -1.8550    0.3716 N   0  0  0  0  0  0  0  0  0  0  0  0
    7.0387   -0.6711   -1.7221 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.2519   -0.0272   -1.6131 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.2892    0.2732    0.4411 C   0  0  1  0  0  0  0  0  0  0  0  0
    7.1312    1.3148    0.0673 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.8778    0.5411    0.0720 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3090    1.6412    0.0384 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7139    0.3154   -0.2563 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.7223   -0.6076   -0.1219 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5539   -1.7274   -0.9306 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.6180   -1.7852   -1.7994 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3551   -2.9429   -1.7340 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9231   -3.2189   -0.3574 C   0  0  1  0  0  0  0  0  0  0  0  0
   -5.5478   -4.4786   -0.4282 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7881   -3.2384    0.6172 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.7328   -4.4936    1.2087 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4625   -2.9336   -0.0152 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.9546   -3.9860   -0.7668 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3776    1.6393   -0.6576 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.5596    1.4256   -1.3378 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0844    4.6192    1.0852 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9763    4.2579    1.5686 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4258    5.9292    1.0058 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0992    8.3279    1.2562 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0003    8.1684   -0.5115 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4024    5.6637   -0.3647 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7776    3.2790   -0.2187 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3765    1.6447    1.2180 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6911    0.0647    1.9162 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9115    0.8807    0.5130 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6206    0.4912    2.2596 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3608   -3.5614    1.9387 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9793   -3.6966   -0.0999 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.4041   -2.8162   -0.0531 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.4569   -1.5237    0.0803 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.1168   -1.6340   -2.2594 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.2481   -0.0179   -2.1697 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.2087    0.8352   -2.1307 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.3367    0.0713    1.5360 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.8008    1.5346    0.7559 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9332    0.0309   -0.9770 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6251   -1.6268   -1.5171 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8474   -3.8375   -2.1299 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2490   -2.7892   -2.4032 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6612   -2.4578   -0.0613 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3267   -4.4097   -1.0355 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9446   -2.4623    1.4180 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3492   -4.4808    1.9833 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7490   -2.7096    0.8004 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4271   -4.8143   -0.4552 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6439    2.2534   -1.2192 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4007    1.6025   -2.3052 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 11 10  1  6
 11 12  2  0
 11 13  1  0
 11 14  1  0
 14 15  1  0
 15 16  2  0
 16 17  1  0
 16 18  1  0
 18 19  1  1
 18 20  1  0
 20 21  1  0
 18 22  1  0
 22 23  1  0
 22 24  1  0
 24 25  2  0
  8 26  1  0
 26 27  1  0
 27 28  1  0
 28 29  1  0
 29 30  1  0
 30 31  1  0
 31 32  1  0
 31 33  1  0
 33 34  1  0
 33 35  1  0
 35 36  1  0
 26 37  1  0
 37 38  1  0
  5 39  1  0
 39 40  2  0
 39 41  1  0
 41  2  2  0
 37  6  1  0
 24 15  1  0
 35 28  1  0
  1 42  1  0
  1 43  1  0
  3 44  1  0
  4 45  1  0
  6 46  1  1
  8 47  1  1
  9 48  1  0
  9 49  1  0
 13 50  1  0
 17 51  1  0
 19 52  1  0
 19 53  1  0
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 21 56  1  0
 22 57  1  1
 23 58  1  0
 26 59  1  6
 28 60  1  6
 30 61  1  0
 30 62  1  0
 31 63  1  1
 32 64  1  0
 33 65  1  1
 34 66  1  0
 35 67  1  1
 36 68  1  0
 37 69  1  6
 38 70  1  0
M  END

HEADER    PROTEIN                                 24-JUN-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-JUN-21         0                                  
HETATM    1  N   UNK     0      -3.927   7.722   0.426  0.00  0.00           N+0
HETATM    2  C   UNK     0      -3.602   6.340   0.494  0.00  0.00           C+0
HETATM    3  C   UNK     0      -4.462   5.354   0.046  0.00  0.00           C+0
HETATM    4  C   UNK     0      -4.087   4.015   0.138  0.00  0.00           C+0
HETATM    5  N   UNK     0      -2.906   3.644   0.655  0.00  0.00           N+0
HETATM    6  C   UNK     0      -2.596   2.249   0.715  0.00  0.00           C+0
HETATM    7  O   UNK     0      -1.396   1.977   1.340  0.00  0.00           O+0
HETATM    8  C   UNK     0      -1.174   0.643   1.117  0.00  0.00           C+0
HETATM    9  C   UNK     0       0.304   0.280   1.224  0.00  0.00           C+0
HETATM   10  O   UNK     0       0.472  -1.095   0.986  0.00  0.00           O+0
HETATM   11  P   UNK     0       2.084  -1.541   1.093  0.00  0.00           P+0
HETATM   12  O   UNK     0       2.713  -1.029   2.355  0.00  0.00           O+0
HETATM   13  O   UNK     0       2.137  -3.248   1.032  0.00  0.00           O+0
HETATM   14  O   UNK     0       2.886  -0.979  -0.305  0.00  0.00           O+0
HETATM   15  C   UNK     0       4.280  -0.744  -0.247  0.00  0.00           C+0
HETATM   16  C   UNK     0       5.233  -1.630  -0.465  0.00  0.00           C+0
HETATM   17  O   UNK     0       4.945  -2.962  -0.793  0.00  0.00           O+0
HETATM   18  C   UNK     0       6.551  -0.996  -0.310  0.00  0.00           C+0
HETATM   19  N   UNK     0       7.503  -1.855   0.372  0.00  0.00           N+0
HETATM   20  C   UNK     0       7.039  -0.671  -1.722  0.00  0.00           C+0
HETATM   21  O   UNK     0       8.252  -0.027  -1.613  0.00  0.00           O+0
HETATM   22  C   UNK     0       6.289   0.273   0.441  0.00  0.00           C+0
HETATM   23  O   UNK     0       7.131   1.315   0.067  0.00  0.00           O+0
HETATM   24  C   UNK     0       4.878   0.541   0.072  0.00  0.00           C+0
HETATM   25  O   UNK     0       4.309   1.641   0.038  0.00  0.00           O+0
HETATM   26  C   UNK     0      -1.714   0.315  -0.256  0.00  0.00           C+0
HETATM   27  O   UNK     0      -2.722  -0.608  -0.122  0.00  0.00           O+0
HETATM   28  C   UNK     0      -2.554  -1.727  -0.931  0.00  0.00           C+0
HETATM   29  O   UNK     0      -3.618  -1.785  -1.799  0.00  0.00           O+0
HETATM   30  C   UNK     0      -4.355  -2.943  -1.734  0.00  0.00           C+0
HETATM   31  C   UNK     0      -4.923  -3.219  -0.357  0.00  0.00           C+0
HETATM   32  O   UNK     0      -5.548  -4.479  -0.428  0.00  0.00           O+0
HETATM   33  C   UNK     0      -3.788  -3.238   0.617  0.00  0.00           C+0
HETATM   34  O   UNK     0      -3.733  -4.494   1.209  0.00  0.00           O+0
HETATM   35  C   UNK     0      -2.462  -2.934  -0.015  0.00  0.00           C+0
HETATM   36  O   UNK     0      -1.955  -3.986  -0.767  0.00  0.00           O+0
HETATM   37  C   UNK     0      -2.378   1.639  -0.658  0.00  0.00           C+0
HETATM   38  O   UNK     0      -3.560   1.426  -1.338  0.00  0.00           O+0
HETATM   39  C   UNK     0      -2.084   4.619   1.085  0.00  0.00           C+0
HETATM   40  O   UNK     0      -0.976   4.258   1.569  0.00  0.00           O+0
HETATM   41  N   UNK     0      -2.426   5.929   1.006  0.00  0.00           N+0
HETATM   42  H   UNK     0      -4.099   8.328   1.256  0.00  0.00           H+0
HETATM   43  H   UNK     0      -4.000   8.168  -0.511  0.00  0.00           H+0
HETATM   44  H   UNK     0      -5.402   5.664  -0.365  0.00  0.00           H+0
HETATM   45  H   UNK     0      -4.778   3.279  -0.219  0.00  0.00           H+0
HETATM   46  H   UNK     0      -3.377   1.645   1.218  0.00  0.00           H+0
HETATM   47  H   UNK     0      -1.691   0.065   1.916  0.00  0.00           H+0
HETATM   48  H   UNK     0       0.912   0.881   0.513  0.00  0.00           H+0
HETATM   49  H   UNK     0       0.621   0.491   2.260  0.00  0.00           H+0
HETATM   50  H   UNK     0       2.361  -3.561   1.939  0.00  0.00           H+0
HETATM   51  H   UNK     0       4.979  -3.697  -0.100  0.00  0.00           H+0
HETATM   52  H   UNK     0       7.404  -2.816  -0.053  0.00  0.00           H+0
HETATM   53  H   UNK     0       8.457  -1.524   0.080  0.00  0.00           H+0
HETATM   54  H   UNK     0       7.117  -1.634  -2.259  0.00  0.00           H+0
HETATM   55  H   UNK     0       6.248  -0.018  -2.170  0.00  0.00           H+0
HETATM   56  H   UNK     0       8.209   0.835  -2.131  0.00  0.00           H+0
HETATM   57  H   UNK     0       6.337   0.071   1.536  0.00  0.00           H+0
HETATM   58  H   UNK     0       7.801   1.535   0.756  0.00  0.00           H+0
HETATM   59  H   UNK     0      -0.933   0.031  -0.977  0.00  0.00           H+0
HETATM   60  H   UNK     0      -1.625  -1.627  -1.517  0.00  0.00           H+0
HETATM   61  H   UNK     0      -3.847  -3.837  -2.130  0.00  0.00           H+0
HETATM   62  H   UNK     0      -5.249  -2.789  -2.403  0.00  0.00           H+0
HETATM   63  H   UNK     0      -5.661  -2.458  -0.061  0.00  0.00           H+0
HETATM   64  H   UNK     0      -6.327  -4.410  -1.036  0.00  0.00           H+0
HETATM   65  H   UNK     0      -3.945  -2.462   1.418  0.00  0.00           H+0
HETATM   66  H   UNK     0      -4.349  -4.481   1.983  0.00  0.00           H+0
HETATM   67  H   UNK     0      -1.749  -2.710   0.800  0.00  0.00           H+0
HETATM   68  H   UNK     0      -2.427  -4.814  -0.455  0.00  0.00           H+0
HETATM   69  H   UNK     0      -1.644   2.253  -1.219  0.00  0.00           H+0
HETATM   70  H   UNK     0      -3.401   1.603  -2.305  0.00  0.00           H+0
CONECT    1    2   42   43                                                  
CONECT    2    1    3   41                                                  
CONECT    3    2    4   44                                                  
CONECT    4    3    5   45                                                  
CONECT    5    4    6   39                                                  
CONECT    6    5    7   37   46                                             
CONECT    7    6    8                                                       
CONECT    8    7    9   26   47                                             
CONECT    9    8   10   48   49                                             
CONECT   10    9   11                                                       
CONECT   11   10   12   13   14                                             
CONECT   12   11                                                            
CONECT   13   11   50                                                       
CONECT   14   11   15                                                       
CONECT   15   14   16   24                                                  
CONECT   16   15   17   18                                                  
CONECT   17   16   51                                                       
CONECT   18   16   19   20   22                                             
CONECT   19   18   52   53                                                  
CONECT   20   18   21   54   55                                             
CONECT   21   20   56                                                       
CONECT   22   18   23   24   57                                             
CONECT   23   22   58                                                       
CONECT   24   22   25   15                                                  
CONECT   25   24                                                            
CONECT   26    8   27   37   59                                             
CONECT   27   26   28                                                       
CONECT   28   27   29   35   60                                             
CONECT   29   28   30                                                       
CONECT   30   29   31   61   62                                             
CONECT   31   30   32   33   63                                             
CONECT   32   31   64                                                       
CONECT   33   31   34   35   65                                             
CONECT   34   33   66                                                       
CONECT   35   33   36   28   67                                             
CONECT   36   35   68                                                       
CONECT   37   26   38    6   69                                             
CONECT   38   37   70                                                       
CONECT   39    5   40   41                                                  
CONECT   40   39                                                            
CONECT   41   39    2                                                       
CONECT   42    1                                                            
CONECT   43    1                                                            
CONECT   44    3                                                            
CONECT   45    4                                                            
CONECT   46    6                                                            
CONECT   47    8                                                            
CONECT   48    9                                                            
CONECT   49    9                                                            
CONECT   50   13                                                            
CONECT   51   17                                                            
CONECT   52   19                                                            
CONECT   53   19                                                            
CONECT   54   20                                                            
CONECT   55   20                                                            
CONECT   56   21                                                            
CONECT   57   22                                                            
CONECT   58   23                                                            
CONECT   59   26                                                            
CONECT   60   28                                                            
CONECT   61   30                                                            
CONECT   62   30                                                            
CONECT   63   31                                                            
CONECT   64   32                                                            
CONECT   65   33                                                            
CONECT   66   34                                                            
CONECT   67   35                                                            
CONECT   68   36                                                            
CONECT   69   37                                                            
CONECT   70   38                                                            
MASTER        0    0    0    0    0    0    0    0   70    0  146    0
END

RDKit          3D

70 73  0  0  0  0  0  0  0  0999 V2000
   -3.9271    7.7218    0.4263 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6024    6.3398    0.4939 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4618    5.3539    0.0455 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0869    4.0151    0.1384 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9056    3.6443    0.6547 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5958    2.2491    0.7147 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.3963    1.9766    1.3404 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1737    0.6425    1.1170 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.3037    0.2798    1.2236 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4716   -1.0952    0.9861 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0842   -1.5410    1.0932 P   0  0  1  0  0  5  0  0  0  0  0  0
    2.7135   -1.0287    2.3547 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1370   -3.2485    1.0324 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8860   -0.9786   -0.3053 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2797   -0.7443   -0.2469 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2332   -1.6296   -0.4649 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9454   -2.9625   -0.7929 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.5509   -0.9963   -0.3104 C   0  0  1  0  0  0  0  0  0  0  0  0
    7.5025   -1.8550    0.3716 N   0  0  0  0  0  0  0  0  0  0  0  0
    7.0387   -0.6711   -1.7221 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.2519   -0.0272   -1.6131 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.2892    0.2732    0.4411 C   0  0  1  0  0  0  0  0  0  0  0  0
    7.1312    1.3148    0.0673 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.8778    0.5411    0.0720 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3090    1.6412    0.0384 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7139    0.3154   -0.2563 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.7223   -0.6076   -0.1219 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5539   -1.7274   -0.9306 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.6180   -1.7852   -1.7994 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3551   -2.9429   -1.7340 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9231   -3.2189   -0.3574 C   0  0  1  0  0  0  0  0  0  0  0  0
   -5.5478   -4.4786   -0.4282 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7881   -3.2384    0.6172 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.7328   -4.4936    1.2087 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4625   -2.9336   -0.0152 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.9546   -3.9860   -0.7668 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3776    1.6393   -0.6576 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.5596    1.4256   -1.3378 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0844    4.6192    1.0852 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9763    4.2579    1.5686 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4258    5.9292    1.0058 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0992    8.3279    1.2562 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0003    8.1684   -0.5115 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4024    5.6637   -0.3647 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7776    3.2790   -0.2187 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3765    1.6447    1.2180 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6911    0.0647    1.9162 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9115    0.8807    0.5130 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6206    0.4912    2.2596 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3608   -3.5614    1.9387 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9793   -3.6966   -0.0999 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.4041   -2.8162   -0.0531 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.4569   -1.5237    0.0803 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.1168   -1.6340   -2.2594 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.2481   -0.0179   -2.1697 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.2087    0.8352   -2.1307 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.3367    0.0713    1.5360 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.8008    1.5346    0.7559 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9332    0.0309   -0.9770 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6251   -1.6268   -1.5171 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8474   -3.8375   -2.1299 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2490   -2.7892   -2.4032 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6612   -2.4578   -0.0613 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3267   -4.4097   -1.0355 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9446   -2.4623    1.4180 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3492   -4.4808    1.9833 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7490   -2.7096    0.8004 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4271   -4.8143   -0.4552 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6439    2.2534   -1.2192 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4007    1.6025   -2.3052 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 11 10  1  6
 11 12  2  0
 11 13  1  0
 11 14  1  0
 14 15  1  0
 15 16  2  0
 16 17  1  0
 16 18  1  0
 18 19  1  1
 18 20  1  0
 20 21  1  0
 18 22  1  0
 22 23  1  0
 22 24  1  0
 24 25  2  0
  8 26  1  0
 26 27  1  0
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  5 39  1  0
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 41  2  2  0
 37  6  1  0
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  1 42  1  0
  1 43  1  0
  3 44  1  0
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  8 47  1  1
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M  END

View in JSmol View NMR Assignments

Synonyms

Value	Source
{[(3R,4R)-3-amino-2,4-dihydroxy-3-(hydroxymethyl)-5-oxocyclopent-1-en-1-yl]oxy}({[(2R,3S,4R,5R)-4-hydroxy-5-(2-hydroxy-4-imino-1,4-dihydropyrimidin-1-yl)-3-{[(3R,5R)-3,4,5-trihydroxyoxan-2-yl]oxy}oxolan-2-yl]methoxy})phosphinate	Generator

Chemical Formula

C₂₀H₂₉N₄O₁₆P

Average Mass

612.4380 Da

Monoisotopic Mass

612.13162 Da

IUPAC Name

{[(3R,4R)-3-amino-2,4-dihydroxy-3-(hydroxymethyl)-5-oxocyclopent-1-en-1-yl]oxy}({[(2R,3S,4R,5R)-5-(4-amino-2-oxo-1,2-dihydropyrimidin-1-yl)-4-hydroxy-3-{[(2S,3R,4R,5R)-3,4,5-trihydroxyoxan-2-yl]oxy}oxolan-2-yl]methoxy})phosphinic acid

Traditional Name

[(3R,4R)-3-amino-2,4-dihydroxy-3-(hydroxymethyl)-5-oxocyclopent-1-en-1-yl]oxy([(2R,3S,4R,5R)-5-(4-amino-2-oxopyrimidin-1-yl)-4-hydroxy-3-{[(2S,3R,4R,5R)-3,4,5-trihydroxyoxan-2-yl]oxy}oxolan-2-yl]methoxy)phosphinic acid

CAS Registry Number

Not Available

SMILES

NC1=NC(=O)N(C=C1)[C@@H]1O[C@H](COP(O)(=O)OC2=C(O)[C@@](N)(CO)[C@@H](O)C2=O)[C@@H](OC2OC[C@@H](O)C(O)[C@H]2O)[C@H]1O

InChI Identifier

InChI=1S/C20H29N4O16P/c21-8-1-2-24(19(33)23-8)17-12(30)13(39-18-10(28)9(27)6(26)3-36-18)7(38-17)4-37-41(34,35)40-14-11(29)15(31)20(22,5-25)16(14)32/h1-2,6-7,9-10,12-13,15,17-18,25-28,30-32H,3-5,22H2,(H,34,35)(H2,21,23,33)/t6-,7-,9?,10-,12-,13-,15+,17-,18?,20-/m1/s1

InChI Key

YUMCOBIDABFYCR-HHLCLMOPSA-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, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, 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
Rhizobium	NPAtlas	29348528

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pyrimidine ribonucleoside monophosphates. These are pyrimidine ribobucleotides with monophosphate group linked to the ribose moiety.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Pyrimidine nucleotides

Sub Class

Pyrimidine ribonucleotides

Direct Parent

Pyrimidine ribonucleoside monophosphates

Alternative Parents

Substituents

Pyrimidine ribonucleoside monophosphate
Pentose-5-phosphate
Pentose phosphate
O-glycosyl compound
N-glycosyl compound
Glycosyl compound
Monosaccharide phosphate
Hydroxypyrimidine
Monoalkyl phosphate
Alkyl phosphate
Pyrimidine
Phosphoric acid ester
Oxane
Organic phosphoric acid derivative
Monosaccharide
Hydropyrimidine
Heteroaromatic compound
Vinylogous acid
Tetrahydrofuran
Cyclic ketone
Secondary alcohol
Ketone
Oxacycle
Azacycle
Organoheterocyclic compound
Polyol
Acetal
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Primary amine
Primary alcohol
Organooxygen compound
Organonitrogen compound
Primary aliphatic amine
Carbonyl group
Amine
Alcohol
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	-2.2	ALOGPS
logP	-7.6	ChemAxon
logS	-1.3	ALOGPS
pKa (Strongest Acidic)	1.22	ChemAxon
pKa (Strongest Basic)	8.57	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	17	ChemAxon
Hydrogen Donor Count	10	ChemAxon
Polar Surface Area	326.84 Å²	ChemAxon
Rotatable Bond Count	9	ChemAxon
Refractivity	127.23 m³·mol⁻¹	ChemAxon
Polarizability	55 Å³	ChemAxon
Number of Rings	4	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	ChemAxon

External Links

NPAtlas ID

NPA021727

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

78443619

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

139589505

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Elvin CM, Asenstorfer RE, Ryder MH, Donner SC, Jones GP, Tate ME: Agrocin 108 is a 5'-cytidine nucleotide bacteriocin containing a carbocyclic phosphoryl-ascorbate group. J Antibiot (Tokyo). 2018 Mar;71(4):438-446. doi: 10.1038/s41429-017-0014-y. Epub 2018 Jan 18. [PubMed:29348528 ]

Showing NP-Card for Agrocin 108 (NP0017486)

MOL for NP0017486 (Agrocin 108)

3D MOL for NP0017486 (Agrocin 108)

3D SDF for NP0017486 (Agrocin 108)

3D-SDF for NP0017486 (Agrocin 108)

PDB for NP0017486 (Agrocin 108)

3D PDB for NP0017486 (Agrocin 108)

SMILES for NP0017486 (Agrocin 108)

INCHI for NP0017486 (Agrocin 108)

Structure for NP0017486 (Agrocin 108)

3D Structure for NP0017486 (Agrocin 108)