NP-MRD: Showing NP-Card for D778-6 (NP0022940)

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Record Information

Version

2.0

Created at

2021-01-06 08:05:20 UTC

Updated at

2021-07-15 17:40:24 UTC

NP-MRD ID

NP0022940

Secondary Accession Numbers

None

Natural Product Identification

Common Name

D778-6

Provided By

NPAtlas

Description

Rhodomycin D is also known as rhodomycinone D. Rhodomycin D is a primary metabolite. Primary metabolites are metabolically or physiologically essential metabolites. They are directly involved in an organism’s growth, development or reproduction. D778-6 is found in Streptomyces. D778-6 was first documented in 1992 (PMID: 1473988). Based on a literature review a small amount of articles have been published on Rhodomycin D (PMID: 10631513) (PMID: 16545946) (PMID: 9098063).

Structure

MOL 3D MOL SDF 3D SDF PDB SMILES InChI


  Mrv1652306242105383D          

 71 75  0  0  0  0            999 V2000
    0.3913    5.2220   -0.7133 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4213    3.9211   -1.3972 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.0061    2.7037   -0.7067 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.1838    1.6478   -1.6732 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8300    2.2738    0.4821 C   0  0  1  0  0  0  0  0  0  0  0  0
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    1.6356    0.3394   -0.5980 O   0  0  0  0  0  0  0  0  0  0  0  0
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    2.9314   -1.6165   -0.7694 C   0  0  1  0  0  0  0  0  0  0  0  0
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 33 68  1  0  0  0  0
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 35 70  1  0  0  0  0
 37 71  1  0  0  0  0
M  END

     RDKit          3D

 71 75  0  0  0  0  0  0  0  0999 V2000
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 23 63  1  0
 25 64  1  6
 29 65  1  0
 29 66  1  0
 29 67  1  0
 33 68  1  0
 34 69  1  0
 35 70  1  0
 37 71  1  0
M  END


  Mrv1652306242105383D          

 71 75  0  0  0  0            999 V2000
    0.3913    5.2220   -0.7133 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4213    3.9211   -1.3972 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.0061    2.7037   -0.7067 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.1838    1.6478   -1.6732 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8300    2.2738    0.4821 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.8317    0.7291    0.4683 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.6356    0.3394   -0.5980 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8358   -0.2536   -0.2223 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.9314   -1.6165   -0.7694 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.9809   -1.8429   -1.8285 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.0901   -3.2759   -2.0370 N   0  0  2  0  0  0  0  0  0  0  0  0
    5.3015   -1.2219   -1.4564 C   0  0  2  0  0  0  0  0  0  0  0  0
    6.0526   -2.1971   -0.8092 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.1540   -0.0481   -0.5367 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.5280   -0.4171    0.8857 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9284    0.5258   -0.5201 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5686    0.2830    0.3709 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7694   -1.0931    0.6902 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3205   -1.8225    1.0572 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0714   -1.5800    0.6016 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1173   -0.7694    0.2234 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8760    0.5745   -0.0799 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9254    1.3640   -0.4524 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5971    1.0784    0.0005 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4409    2.5491   -0.3159 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.8969    3.2841    0.8538 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2208    2.7025    1.9237 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9987    4.6539    0.8450 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4280    5.4467    1.9149 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4632   -1.2782    0.1329 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3981   -0.5053   -0.2175 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6979   -2.6800    0.4525 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9889   -3.1768    0.3681 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2384   -4.4839    0.6612 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2307   -5.3187    1.0394 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8982   -4.8673    1.1422 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9359   -5.7347    1.5214 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6661   -3.5258    0.8374 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3218   -2.9961    0.9223 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3448   -3.6979    1.2615 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4789    5.8148   -1.0318 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5912    5.2145    0.3752 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2692    5.8329   -1.1195 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4463    3.7445   -1.8131 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2265    4.0193   -2.3270 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4651    1.7629   -2.4072 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8768    2.6120    0.3441 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4705    2.6670    1.4366 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3456    0.4461    1.4015 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8517   -0.3156    0.9059 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0996   -2.3467    0.0765 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9178   -1.9190   -1.1714 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5871   -1.4180   -2.7758 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9332   -3.4991   -2.6444 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2620   -3.5570   -2.6391 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8416   -0.9605   -2.3841 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.0242   -2.1021   -0.9815 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8872    0.7211   -0.8578 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8579    0.4597    1.4796 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.4092   -1.1055    0.8539 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7216   -0.9360    1.4246 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5639   -2.6954    1.3209 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9161    2.3227   -0.6917 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0374    2.7791   -1.2369 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8770    4.7608    2.6738 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2462    6.0976    1.5556 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6184    6.0661    2.3202 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7644   -2.4781    0.0626 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.2471   -4.8722    0.5952 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3987   -6.3593    1.2778 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9971   -5.6531    1.6542 H   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  6  0  0  0
  3  5  1  0  0  0  0
  5  6  1  0  0  0  0
  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
 10 11  1  0  0  0  0
 10 12  1  0  0  0  0
 12 13  1  0  0  0  0
 12 14  1  0  0  0  0
 14 15  1  0  0  0  0
 14 16  1  0  0  0  0
  6 17  1  0  0  0  0
 17 18  2  0  0  0  0
 18 19  1  0  0  0  0
 18 20  1  0  0  0  0
 20 21  2  0  0  0  0
 21 22  1  0  0  0  0
 22 23  1  0  0  0  0
 22 24  2  0  0  0  0
 24 25  1  0  0  0  0
 25 26  1  0  0  0  0
 26 27  2  0  0  0  0
 26 28  1  0  0  0  0
 28 29  1  0  0  0  0
 21 30  1  0  0  0  0
 30 31  2  0  0  0  0
 30 32  1  0  0  0  0
 32 33  2  0  0  0  0
 33 34  1  0  0  0  0
 34 35  2  0  0  0  0
 35 36  1  0  0  0  0
 36 37  1  0  0  0  0
 36 38  2  0  0  0  0
 38 39  1  0  0  0  0
 39 40  2  0  0  0  0
 25  3  1  0  0  0  0
 38 32  1  0  0  0  0
 16  8  1  0  0  0  0
 24 17  1  0  0  0  0
 39 20  1  0  0  0  0
  1 41  1  0  0  0  0
  1 42  1  0  0  0  0
  1 43  1  0  0  0  0
  2 44  1  0  0  0  0
  2 45  1  0  0  0  0
  4 46  1  0  0  0  0
  5 47  1  0  0  0  0
  5 48  1  0  0  0  0
  6 49  1  1  0  0  0
  8 50  1  1  0  0  0
  9 51  1  0  0  0  0
  9 52  1  0  0  0  0
 10 53  1  6  0  0  0
 11 54  1  0  0  0  0
 11 55  1  0  0  0  0
 12 56  1  6  0  0  0
 13 57  1  0  0  0  0
 14 58  1  6  0  0  0
 15 59  1  0  0  0  0
 15 60  1  0  0  0  0
 15 61  1  0  0  0  0
 19 62  1  0  0  0  0
 23 63  1  0  0  0  0
 25 64  1  6  0  0  0
 29 65  1  0  0  0  0
 29 66  1  0  0  0  0
 29 67  1  0  0  0  0
 33 68  1  0  0  0  0
 34 69  1  0  0  0  0
 35 70  1  0  0  0  0
 37 71  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0022940

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H]OC1=C2C(=O)C3=C(C(=O)C2=C([H])C([H])=C1[H])C(O[H])=C1C(=C3O[H])[C@@]([H])(O[C@]2([H])O[C@@]([H])(C([H])([H])[H])[C@@]([H])(O[H])[C@@]([H])(N([H])[H])C2([H])[H])C([H])([H])[C@](O[H])(C([H])([H])C([H])([H])[H])[C@]1([H])C(=O)OC([H])([H])[H]

> <INCHI_IDENTIFIER>
InChI=1S/C28H31NO11/c1-4-28(37)9-14(40-15-8-12(29)22(31)10(2)39-15)17-18(21(28)27(36)38-3)26(35)19-20(25(17)34)24(33)16-11(23(19)32)6-5-7-13(16)30/h5-7,10,12,14-15,21-22,30-31,34-35,37H,4,8-9,29H2,1-3H3/t10-,12-,14-,15-,21-,22+,28+/m0/s1

> <INCHI_KEY>
CADJZGPRUYOSGU-QWWLYEKJSA-N

> <FORMULA>
C28H31NO11

> <MOLECULAR_WEIGHT>
557.552

> <EXACT_MASS>
557.189710822

> <JCHEM_ACCEPTOR_COUNT>
11

> <JCHEM_ATOM_COUNT>
71

> <JCHEM_AVERAGE_POLARIZABILITY>
56.91372335879169

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
methyl (1R,2R,4S)-4-{[(2R,4S,5S,6S)-4-amino-5-hydroxy-6-methyloxan-2-yl]oxy}-2-ethyl-2,5,7,12-tetrahydroxy-6,11-dioxo-1,2,3,4,6,11-hexahydrotetracene-1-carboxylate

> <ALOGPS_LOGP>
1.43

> <JCHEM_LOGP>
2.029526012194235

> <ALOGPS_LOGS>
-2.65

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
8.3710873802805

> <JCHEM_PKA_STRONGEST_ACIDIC>
7.738951192803724

> <JCHEM_PKA_STRONGEST_BASIC>
9.949358662255287

> <JCHEM_POLAR_SURFACE_AREA>
206.07

> <JCHEM_REFRACTIVITY>
138.75089999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.24e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
rhodomycin D

> <JCHEM_VEBER_RULE>
0

$$$$

     RDKit          3D

 71 75  0  0  0  0  0  0  0  0999 V2000
    0.3913    5.2220   -0.7133 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4213    3.9211   -1.3972 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0061    2.7037   -0.7067 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.1838    1.6478   -1.6732 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8300    2.2738    0.4821 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8317    0.7291    0.4683 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.6356    0.3394   -0.5980 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8358   -0.2536   -0.2223 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.9314   -1.6165   -0.7694 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9809   -1.8429   -1.8285 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.0901   -3.2759   -2.0370 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.3015   -1.2219   -1.4564 C   0  0  2  0  0  0  0  0  0  0  0  0
    6.0526   -2.1971   -0.8092 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.1540   -0.0481   -0.5367 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.5280   -0.4171    0.8857 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9284    0.5258   -0.5201 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5686    0.2830    0.3709 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7694   -1.0931    0.6902 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3205   -1.8225    1.0572 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0714   -1.5800    0.6016 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1173   -0.7694    0.2234 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8760    0.5745   -0.0799 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9254    1.3640   -0.4524 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5971    1.0784    0.0005 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4409    2.5491   -0.3159 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.8969    3.2841    0.8538 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2208    2.7025    1.9237 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9987    4.6539    0.8450 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4280    5.4467    1.9149 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4632   -1.2782    0.1329 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3981   -0.5053   -0.2175 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6979   -2.6800    0.4525 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9889   -3.1768    0.3681 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2384   -4.4839    0.6612 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2307   -5.3187    1.0394 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8982   -4.8673    1.1422 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9359   -5.7347    1.5214 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6661   -3.5258    0.8374 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3218   -2.9961    0.9223 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3448   -3.6979    1.2615 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4789    5.8148   -1.0318 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5912    5.2145    0.3752 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2692    5.8329   -1.1195 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4463    3.7445   -1.8131 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2265    4.0193   -2.3270 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4651    1.7629   -2.4072 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8768    2.6120    0.3441 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4705    2.6670    1.4366 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3456    0.4461    1.4015 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8517   -0.3156    0.9059 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0996   -2.3467    0.0765 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9178   -1.9190   -1.1714 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5871   -1.4180   -2.7758 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9332   -3.4991   -2.6444 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2620   -3.5570   -2.6391 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8416   -0.9605   -2.3841 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.0242   -2.1021   -0.9815 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8872    0.7211   -0.8578 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8579    0.4597    1.4796 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.4092   -1.1055    0.8539 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7216   -0.9360    1.4246 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5639   -2.6954    1.3209 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9161    2.3227   -0.6917 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0374    2.7791   -1.2369 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8770    4.7608    2.6738 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2462    6.0976    1.5556 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6184    6.0661    2.3202 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7644   -2.4781    0.0626 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.2471   -4.8722    0.5952 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3987   -6.3593    1.2778 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9971   -5.6531    1.6542 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  6
  3  5  1  0
  5  6  1  0
  6  7  1  0
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  8  9  1  0
  9 10  1  0
 10 11  1  0
 10 12  1  0
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 14 15  1  0
 14 16  1  0
  6 17  1  0
 17 18  2  0
 18 19  1  0
 18 20  1  0
 20 21  2  0
 21 22  1  0
 22 23  1  0
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 21 30  1  0
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 32 33  2  0
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 34 35  2  0
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 16  8  1  0
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  1 41  1  0
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 10 53  1  6
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 29 67  1  0
 33 68  1  0
 34 69  1  0
 35 70  1  0
 37 71  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  C   UNK     0       0.391   5.222  -0.713  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.421   3.921  -1.397  0.00  0.00           C+0
HETATM    3  C   UNK     0      -0.006   2.704  -0.707  0.00  0.00           C+0
HETATM    4  O   UNK     0       0.184   1.648  -1.673  0.00  0.00           O+0
HETATM    5  C   UNK     0       0.830   2.274   0.482  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.832   0.729   0.468  0.00  0.00           C+0
HETATM    7  O   UNK     0       1.636   0.339  -0.598  0.00  0.00           O+0
HETATM    8  C   UNK     0       2.836  -0.254  -0.222  0.00  0.00           C+0
HETATM    9  C   UNK     0       2.931  -1.617  -0.769  0.00  0.00           C+0
HETATM   10  C   UNK     0       3.981  -1.843  -1.829  0.00  0.00           C+0
HETATM   11  N   UNK     0       4.090  -3.276  -2.037  0.00  0.00           N+0
HETATM   12  C   UNK     0       5.301  -1.222  -1.456  0.00  0.00           C+0
HETATM   13  O   UNK     0       6.053  -2.197  -0.809  0.00  0.00           O+0
HETATM   14  C   UNK     0       5.154  -0.048  -0.537  0.00  0.00           C+0
HETATM   15  C   UNK     0       5.528  -0.417   0.886  0.00  0.00           C+0
HETATM   16  O   UNK     0       3.928   0.526  -0.520  0.00  0.00           O+0
HETATM   17  C   UNK     0      -0.569   0.283   0.371  0.00  0.00           C+0
HETATM   18  C   UNK     0      -0.769  -1.093   0.690  0.00  0.00           C+0
HETATM   19  O   UNK     0       0.321  -1.823   1.057  0.00  0.00           O+0
HETATM   20  C   UNK     0      -2.071  -1.580   0.602  0.00  0.00           C+0
HETATM   21  C   UNK     0      -3.117  -0.769   0.223  0.00  0.00           C+0
HETATM   22  C   UNK     0      -2.876   0.575  -0.080  0.00  0.00           C+0
HETATM   23  O   UNK     0      -3.925   1.364  -0.452  0.00  0.00           O+0
HETATM   24  C   UNK     0      -1.597   1.078   0.001  0.00  0.00           C+0
HETATM   25  C   UNK     0      -1.441   2.549  -0.316  0.00  0.00           C+0
HETATM   26  C   UNK     0      -1.897   3.284   0.854  0.00  0.00           C+0
HETATM   27  O   UNK     0      -2.221   2.703   1.924  0.00  0.00           O+0
HETATM   28  O   UNK     0      -1.999   4.654   0.845  0.00  0.00           O+0
HETATM   29  C   UNK     0      -2.428   5.447   1.915  0.00  0.00           C+0
HETATM   30  C   UNK     0      -4.463  -1.278   0.133  0.00  0.00           C+0
HETATM   31  O   UNK     0      -5.398  -0.505  -0.218  0.00  0.00           O+0
HETATM   32  C   UNK     0      -4.698  -2.680   0.453  0.00  0.00           C+0
HETATM   33  C   UNK     0      -5.989  -3.177   0.368  0.00  0.00           C+0
HETATM   34  C   UNK     0      -6.238  -4.484   0.661  0.00  0.00           C+0
HETATM   35  C   UNK     0      -5.231  -5.319   1.039  0.00  0.00           C+0
HETATM   36  C   UNK     0      -3.898  -4.867   1.142  0.00  0.00           C+0
HETATM   37  O   UNK     0      -2.936  -5.735   1.521  0.00  0.00           O+0
HETATM   38  C   UNK     0      -3.666  -3.526   0.837  0.00  0.00           C+0
HETATM   39  C   UNK     0      -2.322  -2.996   0.922  0.00  0.00           C+0
HETATM   40  O   UNK     0      -1.345  -3.698   1.262  0.00  0.00           O+0
HETATM   41  H   UNK     0      -0.479   5.815  -1.032  0.00  0.00           H+0
HETATM   42  H   UNK     0       0.591   5.215   0.375  0.00  0.00           H+0
HETATM   43  H   UNK     0       1.269   5.833  -1.119  0.00  0.00           H+0
HETATM   44  H   UNK     0       1.446   3.744  -1.813  0.00  0.00           H+0
HETATM   45  H   UNK     0      -0.227   4.019  -2.327  0.00  0.00           H+0
HETATM   46  H   UNK     0      -0.465   1.763  -2.407  0.00  0.00           H+0
HETATM   47  H   UNK     0       1.877   2.612   0.344  0.00  0.00           H+0
HETATM   48  H   UNK     0       0.471   2.667   1.437  0.00  0.00           H+0
HETATM   49  H   UNK     0       1.346   0.446   1.401  0.00  0.00           H+0
HETATM   50  H   UNK     0       2.852  -0.316   0.906  0.00  0.00           H+0
HETATM   51  H   UNK     0       3.100  -2.347   0.077  0.00  0.00           H+0
HETATM   52  H   UNK     0       1.918  -1.919  -1.171  0.00  0.00           H+0
HETATM   53  H   UNK     0       3.587  -1.418  -2.776  0.00  0.00           H+0
HETATM   54  H   UNK     0       4.933  -3.499  -2.644  0.00  0.00           H+0
HETATM   55  H   UNK     0       3.262  -3.557  -2.639  0.00  0.00           H+0
HETATM   56  H   UNK     0       5.842  -0.961  -2.384  0.00  0.00           H+0
HETATM   57  H   UNK     0       7.024  -2.102  -0.982  0.00  0.00           H+0
HETATM   58  H   UNK     0       5.887   0.721  -0.858  0.00  0.00           H+0
HETATM   59  H   UNK     0       5.858   0.460   1.480  0.00  0.00           H+0
HETATM   60  H   UNK     0       6.409  -1.105   0.854  0.00  0.00           H+0
HETATM   61  H   UNK     0       4.722  -0.936   1.425  0.00  0.00           H+0
HETATM   62  H   UNK     0       0.564  -2.695   1.321  0.00  0.00           H+0
HETATM   63  H   UNK     0      -3.916   2.323  -0.692  0.00  0.00           H+0
HETATM   64  H   UNK     0      -2.037   2.779  -1.237  0.00  0.00           H+0
HETATM   65  H   UNK     0      -2.877   4.761   2.674  0.00  0.00           H+0
HETATM   66  H   UNK     0      -3.246   6.098   1.556  0.00  0.00           H+0
HETATM   67  H   UNK     0      -1.618   6.066   2.320  0.00  0.00           H+0
HETATM   68  H   UNK     0      -6.764  -2.478   0.063  0.00  0.00           H+0
HETATM   69  H   UNK     0      -7.247  -4.872   0.595  0.00  0.00           H+0
HETATM   70  H   UNK     0      -5.399  -6.359   1.278  0.00  0.00           H+0
HETATM   71  H   UNK     0      -1.997  -5.653   1.654  0.00  0.00           H+0
CONECT    1    2   41   42   43                                             
CONECT    2    1    3   44   45                                             
CONECT    3    2    4    5   25                                             
CONECT    4    3   46                                                       
CONECT    5    3    6   47   48                                             
CONECT    6    5    7   17   49                                             
CONECT    7    6    8                                                       
CONECT    8    7    9   16   50                                             
CONECT    9    8   10   51   52                                             
CONECT   10    9   11   12   53                                             
CONECT   11   10   54   55                                                  
CONECT   12   10   13   14   56                                             
CONECT   13   12   57                                                       
CONECT   14   12   15   16   58                                             
CONECT   15   14   59   60   61                                             
CONECT   16   14    8                                                       
CONECT   17    6   18   24                                                  
CONECT   18   17   19   20                                                  
CONECT   19   18   62                                                       
CONECT   20   18   21   39                                                  
CONECT   21   20   22   30                                                  
CONECT   22   21   23   24                                                  
CONECT   23   22   63                                                       
CONECT   24   22   25   17                                                  
CONECT   25   24   26    3   64                                             
CONECT   26   25   27   28                                                  
CONECT   27   26                                                            
CONECT   28   26   29                                                       
CONECT   29   28   65   66   67                                             
CONECT   30   21   31   32                                                  
CONECT   31   30                                                            
CONECT   32   30   33   38                                                  
CONECT   33   32   34   68                                                  
CONECT   34   33   35   69                                                  
CONECT   35   34   36   70                                                  
CONECT   36   35   37   38                                                  
CONECT   37   36   71                                                       
CONECT   38   36   39   32                                                  
CONECT   39   38   40   20                                                  
CONECT   40   39                                                            
CONECT   41    1                                                            
CONECT   42    1                                                            
CONECT   43    1                                                            
CONECT   44    2                                                            
CONECT   45    2                                                            
CONECT   46    4                                                            
CONECT   47    5                                                            
CONECT   48    5                                                            
CONECT   49    6                                                            
CONECT   50    8                                                            
CONECT   51    9                                                            
CONECT   52    9                                                            
CONECT   53   10                                                            
CONECT   54   11                                                            
CONECT   55   11                                                            
CONECT   56   12                                                            
CONECT   57   13                                                            
CONECT   58   14                                                            
CONECT   59   15                                                            
CONECT   60   15                                                            
CONECT   61   15                                                            
CONECT   62   19                                                            
CONECT   63   23                                                            
CONECT   64   25                                                            
CONECT   65   29                                                            
CONECT   66   29                                                            
CONECT   67   29                                                            
CONECT   68   33                                                            
CONECT   69   34                                                            
CONECT   70   35                                                            
CONECT   71   37                                                            
MASTER        0    0    0    0    0    0    0    0   71    0  150    0
END

RDKit          3D

71 75  0  0  0  0  0  0  0  0999 V2000
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   -0.0061    2.7037   -0.7067 C   0  0  1  0  0  0  0  0  0  0  0  0
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    2.8358   -0.2536   -0.2223 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.9314   -1.6165   -0.7694 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9809   -1.8429   -1.8285 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.0901   -3.2759   -2.0370 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.3015   -1.2219   -1.4564 C   0  0  2  0  0  0  0  0  0  0  0  0
    6.0526   -2.1971   -0.8092 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.1540   -0.0481   -0.5367 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.5280   -0.4171    0.8857 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -1.3448   -3.6979    1.2615 O   0  0  0  0  0  0  0  0  0  0  0  0
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    7.0242   -2.1021   -0.9815 H   0  0  0  0  0  0  0  0  0  0  0  0
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    4.7216   -0.9360    1.4246 H   0  0  0  0  0  0  0  0  0  0  0  0
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  1  2  1  0
  2  3  1  0
  3  4  1  6
  3  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 10 12  1  0
 12 13  1  0
 12 14  1  0
 14 15  1  0
 14 16  1  0
  6 17  1  0
 17 18  2  0
 18 19  1  0
 18 20  1  0
 20 21  2  0
 21 22  1  0
 22 23  1  0
 22 24  2  0
 24 25  1  0
 25 26  1  0
 26 27  2  0
 26 28  1  0
 28 29  1  0
 21 30  1  0
 30 31  2  0
 30 32  1  0
 32 33  2  0
 33 34  1  0
 34 35  2  0
 35 36  1  0
 36 37  1  0
 36 38  2  0
 38 39  1  0
 39 40  2  0
 25  3  1  0
 38 32  1  0
 16  8  1  0
 24 17  1  0
 39 20  1  0
  1 41  1  0
  1 42  1  0
  1 43  1  0
  2 44  1  0
  2 45  1  0
  4 46  1  0
  5 47  1  0
  5 48  1  0
  6 49  1  1
  8 50  1  1
  9 51  1  0
  9 52  1  0
 10 53  1  6
 11 54  1  0
 11 55  1  0
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 14 58  1  6
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 15 61  1  0
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 37 71  1  0
M  END

View in JSmol View NMR Assignments

Synonyms

Value	Source
1-Hydroxy-10-methoxycarbonyl-13-deoxocarminomycin	ChEBI
7-O-(3-Amino-2,3,6-trideoxy-alpha-hexopyranosyl)-epsilon-isorhodomycinone	ChEBI
Rhodomycinone D	ChEBI
7-O-(3-Amino-2,3,6-trideoxy-a-hexopyranosyl)-epsilon-isorhodomycinone	Generator
7-O-(3-Amino-2,3,6-trideoxy-α-hexopyranosyl)-epsilon-isorhodomycinone	Generator

Chemical Formula

C₂₈H₃₁NO₁₁

Average Mass

557.5520 Da

Monoisotopic Mass

557.18971 Da

IUPAC Name

methyl (1R,2R,4S)-4-{[(2R,4S,5S,6S)-4-amino-5-hydroxy-6-methyloxan-2-yl]oxy}-2-ethyl-2,5,7,12-tetrahydroxy-6,11-dioxo-1,2,3,4,6,11-hexahydrotetracene-1-carboxylate

Traditional Name

rhodomycin D

CAS Registry Number

Not Available

SMILES

CC[C@@]1(O)C[C@H](O[C@H]2C[C@H](N)[C@H](O)[C@H](C)O2)C2=C(O)C3=C(C(O)=C2[C@H]1C(=O)OC)C(=O)C1=C(C(O)=CC=C1)C3=O

InChI Identifier

InChI=1S/C28H31NO11/c1-4-28(37)9-14(40-15-8-12(29)22(31)10(2)39-15)17-18(21(28)27(36)38-3)26(35)19-20(25(17)34)24(33)16-11(23(19)32)6-5-7-13(16)30/h5-7,10,12,14-15,21-22,30-31,34-35,37H,4,8-9,29H2,1-3H3/t10-,12-,14-,15-,21-,22+,28+/m0/s1

InChI Key

CADJZGPRUYOSGU-QWWLYEKJSA-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
Streptomyces	NPAtlas	8436560

Chemical Taxonomy

Classification

Not classified

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	1.43	ALOGPS
logP	2.03	ChemAxon
logS	-2.6	ALOGPS
pKa (Strongest Acidic)	7.74	ChemAxon
pKa (Strongest Basic)	9.95	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	11	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	206.07 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	138.75 m³·mol⁻¹	ChemAxon
Polarizability	56.91 Å³	ChemAxon
Number of Rings	5	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

NPAtlas ID

NPA017731

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

391923

KEGG Compound ID

C12426

BioCyc ID

CPD-15730

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

443828

PDB ID

Not Available

ChEBI ID

32096

Good Scents ID

Not Available

References

General References

Yoshimoto A, Johdo O, Tone H, Okamoto R, Naganawa H, Sawa T, Takeuchi T: Production of new anthracycline antibiotics 1-hydroxy-oxaunomycin and 6-deoxyoxaunomycin by limited biosynthetic conversion using a daunorubicin-negative mutant. J Antibiot (Tokyo). 1992 Oct;45(10):1609-17. doi: 10.7164/antibiotics.45.1609. [PubMed:1473988 ]
Olano C, Lomovskaya N, Fonstein L, Roll JT, Hutchinson CR: A two-plasmid system for the glycosylation of polyketide antibiotics: bioconversion of epsilon-rhodomycinone to rhodomycin D. Chem Biol. 1999 Dec;6(12):845-55. doi: 10.1016/s1074-5521(00)80004-6. [PubMed:10631513 ]
Jiang H, Hutchinson CR: Feedback regulation of doxorubicin biosynthesis in Streptomyces peucetius. Res Microbiol. 2006 Sep;157(7):666-74. doi: 10.1016/j.resmic.2006.02.004. Epub 2006 Mar 3. [PubMed:16545946 ]
Dickens ML, Priestley ND, Strohl WR: In vivo and in vitro bioconversion of epsilon-rhodomycinone glycoside to doxorubicin: functions of DauP, DauK, and DoxA. J Bacteriol. 1997 Apr;179(8):2641-50. doi: 10.1128/jb.179.8.2641-2650.1997. [PubMed:9098063 ]

Showing NP-Card for D778-6 (NP0022940)

MOL for NP0022940 (D778-6)

3D MOL for NP0022940 (D778-6)

3D SDF for NP0022940 (D778-6)

3D-SDF for NP0022940 (D778-6)

PDB for NP0022940 (D778-6)

3D PDB for NP0022940 (D778-6)

SMILES for NP0022940 (D778-6)

INCHI for NP0022940 (D778-6)

Structure for NP0022940 (D778-6)

3D Structure for NP0022940 (D778-6)