NP-MRD: Showing NP-Card for gentamicin C1a (NP0030291)

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Record Information

Version

1.0

Created at

2021-06-19 21:41:20 UTC

Updated at

2021-06-29 23:58:10 UTC

NP-MRD ID

NP0030291

Secondary Accession Numbers

None

Natural Product Identification

Common Name

gentamicin C1a

Provided By

JEOL Database JEOL Logo

Description

Gentamicin C1a, also known as gentamycin C12, belongs to the class of organic compounds known as aminocyclitol glycosides. These are organic compounds containing an amicocyclitol moiety glycosidically linked to a carbohydrate moiety. There are two major classes of aminoglycosides containing a 2-streptamine core. They are called 4,5- and 4,6-disubstituted 2-deoxystreptamines. Gentamicin C1a is a primary metabolite. Primary metabolites are metabolically or physiologically essential metabolites. They are directly involved in an organism’s growth, development or reproduction. gentamicin C1a is found in Apis cerana. It was first documented in 2014 (PMID: 24858300). Based on a literature review a significant number of articles have been published on Gentamicin C1a (PMID: 34119221) (PMID: 32156271) (PMID: 31847403) (PMID: 30787404) (PMID: 28887556) (PMID: 28786377).

Structure

MOL 3D MOL SDF 3D SDF PDB SMILES InChI


  Mrv1652306192123413D          

 70 72  0  0  0  0            999 V2000
    5.6045    2.3970   -4.9904 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2462    2.3015   -5.5297 N   0  0  1  0  0  0  0  0  0  0  0  0
    3.2106    2.4567   -4.4588 C   0  0  2  0  0  0  0  0  0  0  0  0
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    2.1852    0.3968   -1.4795 O   0  0  0  0  0  0  0  0  0  0  0  0
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M  END

     RDKit          3D

 70 72  0  0  0  0  0  0  0  0999 V2000
    5.6045    2.3970   -4.9904 C   0  0  0  0  0  0  0  0  0  0  0  0
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M  END


  Mrv1652306192123413D          

 70 72  0  0  0  0            999 V2000
    5.6045    2.3970   -4.9904 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2462    2.3015   -5.5297 N   0  0  1  0  0  0  0  0  0  0  0  0
    3.2106    2.4567   -4.4588 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.3451    1.3727   -3.3498 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.1573    1.9260   -2.2870 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9730    0.9255   -2.7936 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.1852    0.3968   -1.4795 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0176   -0.2682   -0.9546 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.5810    0.5108    0.3008 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.1019    1.8142   -0.0866 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5199   -0.2279    1.0879 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.7612    0.4529    2.3350 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8361    1.3997    2.2413 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.0590    0.7917    2.6584 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0940    0.4704    4.0548 C   0  0  2  0  0  0  0  0  0  0  0  0
   -4.4180   -0.2643    4.3720 C   0  0  1  0  0  0  0  0  0  0  0  0
   -5.6325    0.5384    4.2014 N   0  0  1  0  0  0  0  0  0  0  0  0
   -2.8895    1.7216    4.9125 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.5596    2.3844    4.5684 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.4958    2.6755    3.0669 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.1722    3.2448    2.7413 N   0  0  1  0  0  0  0  0  0  0  0  0
   -0.0705   -1.6694    1.4187 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.1158   -2.4030    2.1540 N   0  0  2  0  0  0  0  0  0  0  0  0
    0.2897   -2.4422    0.1485 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.4002   -1.7291   -0.6279 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.7106   -2.4801   -1.8581 N   0  0  1  0  0  0  0  0  0  0  0  0
    1.1145    2.0561   -2.6947 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7063    2.5217   -3.9879 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.7907    2.4004   -5.0884 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.5378    3.4656   -6.1616 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6563    1.1210   -5.7389 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.8604    1.5344   -4.3691 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.3163    2.4091   -5.8223 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.7478    3.3186   -4.4173 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1410    3.0711   -6.1926 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3438    3.4515   -4.0105 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8726    0.4787   -3.7027 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8996    1.4152   -1.4923 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5257    0.1536   -3.4324 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1967   -0.2502   -1.6858 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4446    0.6992    0.9506 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6534    2.1015   -0.8481 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4466   -0.2659    0.4977 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9870    1.7159    1.2031 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2841   -0.2399    4.2633 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5026   -1.1321    3.7079 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3877   -0.6369    5.4021 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4474   -0.0275    4.4314 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6304    1.3220    4.8506 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6886    2.4489    4.7261 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9135    1.4654    5.9774 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4519    3.3123    5.1433 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7367    1.7234    4.8702 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2581    3.4325    2.8424 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5264    2.5338    2.9706 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1059    3.3058    1.7185 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8057   -1.6283    2.0787 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9858   -2.3859    1.6192 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3298   -1.8522    2.9895 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6176   -3.4566    0.4124 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6006   -2.5526   -0.4864 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3173   -1.7217   -0.0248 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0306   -3.4173   -1.6100 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8660   -2.6153   -2.4137 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4182    3.5687   -3.8438 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1949    1.9653   -4.2711 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1590    3.3075   -7.0495 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5003    3.4161   -6.5132 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7226    4.4737   -5.7771 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4981    0.9939   -6.2268 H   0  0  0  0  0  0  0  0  0  0  0  0
  8  9  1  0  0  0  0
  9 11  1  0  0  0  0
 11 22  1  0  0  0  0
  8  7  1  0  0  0  0
 25 26  1  0  0  0  0
 15 16  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 18  1  0  0  0  0
 18 19  1  0  0  0  0
 19 20  1  0  0  0  0
 20 13  1  0  0  0  0
  6  4  1  0  0  0  0
  4  3  1  0  0  0  0
  3 29  1  0  0  0  0
 29 28  1  0  0  0  0
 28 27  1  0  0  0  0
 27  6  1  0  0  0  0
 29 31  1  6  0  0  0
 29 30  1  0  0  0  0
  3  2  1  0  0  0  0
  4  5  1  0  0  0  0
 22 24  1  0  0  0  0
 16 17  1  0  0  0  0
 24 25  1  0  0  0  0
  2  1  1  0  0  0  0
 25  8  1  0  0  0  0
 22 23  1  0  0  0  0
 20 21  1  0  0  0  0
 13 12  1  0  0  0  0
  9 10  1  0  0  0  0
 11 12  1  0  0  0  0
  6  7  1  0  0  0  0
 13 44  1  6  0  0  0
 18 50  1  0  0  0  0
 18 51  1  0  0  0  0
 21 55  1  0  0  0  0
 21 56  1  0  0  0  0
 20 54  1  1  0  0  0
 15 45  1  6  0  0  0
 16 46  1  0  0  0  0
 16 47  1  0  0  0  0
 19 52  1  0  0  0  0
 19 53  1  0  0  0  0
 22 57  1  1  0  0  0
  8 40  1  6  0  0  0
 11 43  1  6  0  0  0
 25 62  1  1  0  0  0
 26 63  1  0  0  0  0
 26 64  1  0  0  0  0
 24 60  1  0  0  0  0
 24 61  1  0  0  0  0
 10 42  1  0  0  0  0
  9 41  1  1  0  0  0
 31 70  1  0  0  0  0
  6 39  1  6  0  0  0
 30 67  1  0  0  0  0
 30 68  1  0  0  0  0
 30 69  1  0  0  0  0
  3 36  1  1  0  0  0
  2 35  1  0  0  0  0
  4 37  1  6  0  0  0
  5 38  1  0  0  0  0
 28 65  1  0  0  0  0
 28 66  1  0  0  0  0
 17 48  1  0  0  0  0
 17 49  1  0  0  0  0
  1 32  1  0  0  0  0
  1 33  1  0  0  0  0
  1 34  1  0  0  0  0
 23 58  1  0  0  0  0
 23 59  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0030291

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H]O[C@@]1([H])[C@@]([H])(O[C@]2([H])[C@@]([H])(O[H])[C@]([H])(O[C@@]3([H])O[C@]([H])(C([H])([H])N([H])[H])C([H])([H])C([H])([H])[C@@]3([H])N([H])[H])[C@@]([H])(N([H])[H])C([H])([H])[C@@]2([H])N([H])[H])OC([H])([H])[C@@](O[H])(C([H])([H])[H])[C@]1([H])N([H])C([H])([H])[H]

> <INCHI_IDENTIFIER>
InChI=1S/C19H39N5O7/c1-19(27)7-28-18(13(26)16(19)24-2)31-15-11(23)5-10(22)14(12(15)25)30-17-9(21)4-3-8(6-20)29-17/h8-18,24-27H,3-7,20-23H2,1-2H3/t8-,9+,10-,11+,12-,13+,14+,15-,16+,17+,18+,19-/m0/s1

> <INCHI_KEY>
VEGXETMJINRLTH-BOZYPMBZSA-N

> <FORMULA>
C19H39N5O7

> <MOLECULAR_WEIGHT>
449.5423

> <EXACT_MASS>
449.284948627

> <JCHEM_ACCEPTOR_COUNT>
12

> <JCHEM_ATOM_COUNT>
70

> <JCHEM_AVERAGE_POLARIZABILITY>
47.351159350515935

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
8

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,3R,4R,5R)-2-{[(1S,2S,3R,4S,6R)-4,6-diamino-3-{[(2R,3R,6S)-3-amino-6-(aminomethyl)oxan-2-yl]oxy}-2-hydroxycyclohexyl]oxy}-5-methyl-4-(methylamino)oxane-3,5-diol

> <ALOGPS_LOGP>
-2.24

> <JCHEM_LOGP>
-3.9863109476666665

> <ALOGPS_LOGS>
-1.34

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
5

> <JCHEM_PKA>
13.159228031928965

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.548486195889797

> <JCHEM_PKA_STRONGEST_BASIC>
9.898564301835346

> <JCHEM_POLAR_SURFACE_AREA>
213.72

> <JCHEM_REFRACTIVITY>
108.8273

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
2.05e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
gentamicin C1A

> <JCHEM_VEBER_RULE>
0

$$$$

     RDKit          3D

 70 72  0  0  0  0  0  0  0  0999 V2000
    5.6045    2.3970   -4.9904 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2462    2.3015   -5.5297 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.2106    2.4567   -4.4588 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.3451    1.3727   -3.3498 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.1573    1.9260   -2.2870 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9730    0.9255   -2.7936 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.1852    0.3968   -1.4795 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0176   -0.2682   -0.9546 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.5810    0.5108    0.3008 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.1019    1.8142   -0.0866 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5199   -0.2279    1.0879 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.7612    0.4529    2.3350 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8361    1.3997    2.2413 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.0590    0.7917    2.6584 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0940    0.4704    4.0548 C   0  0  2  0  0  0  0  0  0  0  0  0
   -4.4180   -0.2643    4.3720 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6325    0.5384    4.2014 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8895    1.7216    4.9125 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5596    2.3844    4.5684 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4958    2.6755    3.0669 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.1722    3.2448    2.7413 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0705   -1.6694    1.4187 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.1158   -2.4030    2.1540 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.2897   -2.4422    0.1485 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4002   -1.7291   -0.6279 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.7106   -2.4801   -1.8581 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.1145    2.0561   -2.6947 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7063    2.5217   -3.9879 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7907    2.4004   -5.0884 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.5378    3.4656   -6.1616 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6563    1.1210   -5.7389 O   0  0  0  0  0  0  0  0  0  0  0  0
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    0.1967   -0.2502   -1.6858 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4446    0.6992    0.9506 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6534    2.1015   -0.8481 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4466   -0.2659    0.4977 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9870    1.7159    1.2031 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2841   -0.2399    4.2633 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5026   -1.1321    3.7079 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3877   -0.6369    5.4021 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4474   -0.0275    4.4314 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6304    1.3220    4.8506 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6886    2.4489    4.7261 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9135    1.4654    5.9774 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4519    3.3123    5.1433 H   0  0  0  0  0  0  0  0  0  0  0  0
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    0.5264    2.5338    2.9706 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1059    3.3058    1.7185 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8057   -1.6283    2.0787 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9858   -2.3859    1.6192 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3298   -1.8522    2.9895 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6176   -3.4566    0.4124 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6006   -2.5526   -0.4864 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3173   -1.7217   -0.0248 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0306   -3.4173   -1.6100 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8660   -2.6153   -2.4137 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4182    3.5687   -3.8438 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1949    1.9653   -4.2711 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1590    3.3075   -7.0495 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5003    3.4161   -6.5132 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7226    4.4737   -5.7771 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4981    0.9939   -6.2268 H   0  0  0  0  0  0  0  0  0  0  0  0
  8  9  1  0
  9 11  1  0
 11 22  1  0
  8  7  1  0
 25 26  1  0
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 27  6  1  0
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 23 59  1  0
M  END

HEADER    PROTEIN                                 19-JUN-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   19-JUN-21         0                                  
HETATM    1  C   UNK     0       5.604   2.397  -4.990  0.00  0.00           C+0
HETATM    2  N   UNK     0       4.246   2.301  -5.530  0.00  0.00           N+0
HETATM    3  C   UNK     0       3.211   2.457  -4.459  0.00  0.00           C+0
HETATM    4  C   UNK     0       3.345   1.373  -3.350  0.00  0.00           C+0
HETATM    5  O   UNK     0       4.157   1.926  -2.287  0.00  0.00           O+0
HETATM    6  C   UNK     0       1.973   0.926  -2.794  0.00  0.00           C+0
HETATM    7  O   UNK     0       2.185   0.397  -1.480  0.00  0.00           O+0
HETATM    8  C   UNK     0       1.018  -0.268  -0.955  0.00  0.00           C+0
HETATM    9  C   UNK     0       0.581   0.511   0.301  0.00  0.00           C+0
HETATM   10  O   UNK     0       0.102   1.814  -0.087  0.00  0.00           O+0
HETATM   11  C   UNK     0      -0.520  -0.228   1.088  0.00  0.00           C+0
HETATM   12  O   UNK     0      -0.761   0.453   2.335  0.00  0.00           O+0
HETATM   13  C   UNK     0      -1.836   1.400   2.241  0.00  0.00           C+0
HETATM   14  O   UNK     0      -3.059   0.792   2.658  0.00  0.00           O+0
HETATM   15  C   UNK     0      -3.094   0.470   4.055  0.00  0.00           C+0
HETATM   16  C   UNK     0      -4.418  -0.264   4.372  0.00  0.00           C+0
HETATM   17  N   UNK     0      -5.633   0.538   4.201  0.00  0.00           N+0
HETATM   18  C   UNK     0      -2.890   1.722   4.912  0.00  0.00           C+0
HETATM   19  C   UNK     0      -1.560   2.384   4.568  0.00  0.00           C+0
HETATM   20  C   UNK     0      -1.496   2.676   3.067  0.00  0.00           C+0
HETATM   21  N   UNK     0      -0.172   3.245   2.741  0.00  0.00           N+0
HETATM   22  C   UNK     0      -0.071  -1.669   1.419  0.00  0.00           C+0
HETATM   23  N   UNK     0      -1.116  -2.403   2.154  0.00  0.00           N+0
HETATM   24  C   UNK     0       0.290  -2.442   0.149  0.00  0.00           C+0
HETATM   25  C   UNK     0       1.400  -1.729  -0.628  0.00  0.00           C+0
HETATM   26  N   UNK     0       1.711  -2.480  -1.858  0.00  0.00           N+0
HETATM   27  O   UNK     0       1.115   2.056  -2.695  0.00  0.00           O+0
HETATM   28  C   UNK     0       0.706   2.522  -3.988  0.00  0.00           C+0
HETATM   29  C   UNK     0       1.791   2.400  -5.088  0.00  0.00           C+0
HETATM   30  C   UNK     0       1.538   3.466  -6.162  0.00  0.00           C+0
HETATM   31  O   UNK     0       1.656   1.121  -5.739  0.00  0.00           O+0
HETATM   32  H   UNK     0       5.860   1.534  -4.369  0.00  0.00           H+0
HETATM   33  H   UNK     0       6.316   2.409  -5.822  0.00  0.00           H+0
HETATM   34  H   UNK     0       5.748   3.319  -4.417  0.00  0.00           H+0
HETATM   35  H   UNK     0       4.141   3.071  -6.193  0.00  0.00           H+0
HETATM   36  H   UNK     0       3.344   3.451  -4.011  0.00  0.00           H+0
HETATM   37  H   UNK     0       3.873   0.479  -3.703  0.00  0.00           H+0
HETATM   38  H   UNK     0       3.900   1.415  -1.492  0.00  0.00           H+0
HETATM   39  H   UNK     0       1.526   0.154  -3.432  0.00  0.00           H+0
HETATM   40  H   UNK     0       0.197  -0.250  -1.686  0.00  0.00           H+0
HETATM   41  H   UNK     0       1.445   0.699   0.951  0.00  0.00           H+0
HETATM   42  H   UNK     0       0.653   2.102  -0.848  0.00  0.00           H+0
HETATM   43  H   UNK     0      -1.447  -0.266   0.498  0.00  0.00           H+0
HETATM   44  H   UNK     0      -1.987   1.716   1.203  0.00  0.00           H+0
HETATM   45  H   UNK     0      -2.284  -0.240   4.263  0.00  0.00           H+0
HETATM   46  H   UNK     0      -4.503  -1.132   3.708  0.00  0.00           H+0
HETATM   47  H   UNK     0      -4.388  -0.637   5.402  0.00  0.00           H+0
HETATM   48  H   UNK     0      -6.447  -0.028   4.431  0.00  0.00           H+0
HETATM   49  H   UNK     0      -5.630   1.322   4.851  0.00  0.00           H+0
HETATM   50  H   UNK     0      -3.689   2.449   4.726  0.00  0.00           H+0
HETATM   51  H   UNK     0      -2.914   1.465   5.977  0.00  0.00           H+0
HETATM   52  H   UNK     0      -1.452   3.312   5.143  0.00  0.00           H+0
HETATM   53  H   UNK     0      -0.737   1.723   4.870  0.00  0.00           H+0
HETATM   54  H   UNK     0      -2.258   3.433   2.842  0.00  0.00           H+0
HETATM   55  H   UNK     0       0.526   2.534   2.971  0.00  0.00           H+0
HETATM   56  H   UNK     0      -0.106   3.306   1.718  0.00  0.00           H+0
HETATM   57  H   UNK     0       0.806  -1.628   2.079  0.00  0.00           H+0
HETATM   58  H   UNK     0      -1.986  -2.386   1.619  0.00  0.00           H+0
HETATM   59  H   UNK     0      -1.330  -1.852   2.990  0.00  0.00           H+0
HETATM   60  H   UNK     0       0.618  -3.457   0.412  0.00  0.00           H+0
HETATM   61  H   UNK     0      -0.601  -2.553  -0.486  0.00  0.00           H+0
HETATM   62  H   UNK     0       2.317  -1.722  -0.025  0.00  0.00           H+0
HETATM   63  H   UNK     0       2.031  -3.417  -1.610  0.00  0.00           H+0
HETATM   64  H   UNK     0       0.866  -2.615  -2.414  0.00  0.00           H+0
HETATM   65  H   UNK     0       0.418   3.569  -3.844  0.00  0.00           H+0
HETATM   66  H   UNK     0      -0.195   1.965  -4.271  0.00  0.00           H+0
HETATM   67  H   UNK     0       2.159   3.308  -7.050  0.00  0.00           H+0
HETATM   68  H   UNK     0       0.500   3.416  -6.513  0.00  0.00           H+0
HETATM   69  H   UNK     0       1.723   4.474  -5.777  0.00  0.00           H+0
HETATM   70  H   UNK     0       2.498   0.994  -6.227  0.00  0.00           H+0
CONECT    1    2   32   33   34                                             
CONECT    2    3    1   35                                                  
CONECT    3    4   29    2   36                                             
CONECT    4    6    3    5   37                                             
CONECT    5    4   38                                                       
CONECT    6    4   27    7   39                                             
CONECT    7    8    6                                                       
CONECT    8    9    7   25   40                                             
CONECT    9    8   11   10   41                                             
CONECT   10    9   42                                                       
CONECT   11    9   22   12   43                                             
CONECT   12   13   11                                                       
CONECT   13   14   20   12   44                                             
CONECT   14   13   15                                                       
CONECT   15   16   14   18   45                                             
CONECT   16   15   17   46   47                                             
CONECT   17   16   48   49                                                  
CONECT   18   15   19   50   51                                             
CONECT   19   18   20   52   53                                             
CONECT   20   19   13   21   54                                             
CONECT   21   20   55   56                                                  
CONECT   22   11   24   23   57                                             
CONECT   23   22   58   59                                                  
CONECT   24   22   25   60   61                                             
CONECT   25   26   24    8   62                                             
CONECT   26   25   63   64                                                  
CONECT   27   28    6                                                       
CONECT   28   29   27   65   66                                             
CONECT   29    3   28   31   30                                             
CONECT   30   29   67   68   69                                             
CONECT   31   29   70                                                       
CONECT   32    1                                                            
CONECT   33    1                                                            
CONECT   34    1                                                            
CONECT   35    2                                                            
CONECT   36    3                                                            
CONECT   37    4                                                            
CONECT   38    5                                                            
CONECT   39    6                                                            
CONECT   40    8                                                            
CONECT   41    9                                                            
CONECT   42   10                                                            
CONECT   43   11                                                            
CONECT   44   13                                                            
CONECT   45   15                                                            
CONECT   46   16                                                            
CONECT   47   16                                                            
CONECT   48   17                                                            
CONECT   49   17                                                            
CONECT   50   18                                                            
CONECT   51   18                                                            
CONECT   52   19                                                            
CONECT   53   19                                                            
CONECT   54   20                                                            
CONECT   55   21                                                            
CONECT   56   21                                                            
CONECT   57   22                                                            
CONECT   58   23                                                            
CONECT   59   23                                                            
CONECT   60   24                                                            
CONECT   61   24                                                            
CONECT   62   25                                                            
CONECT   63   26                                                            
CONECT   64   26                                                            
CONECT   65   28                                                            
CONECT   66   28                                                            
CONECT   67   30                                                            
CONECT   68   30                                                            
CONECT   69   30                                                            
CONECT   70   31                                                            
MASTER        0    0    0    0    0    0    0    0   70    0  144    0
END

RDKit          3D

70 72  0  0  0  0  0  0  0  0999 V2000
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  4 37  1  6
  5 38  1  0
 28 65  1  0
 28 66  1  0
 17 48  1  0
 17 49  1  0
  1 32  1  0
  1 33  1  0
  1 34  1  0
 23 58  1  0
 23 59  1  0
M  END

View in JSmol

Synonyms

Value	Source
Gentamycin C12	ChEBI
O-3-Deoxy-4-C-methyl-3-(methylamino)-beta-L-arabinopyranosyl-(1-6)-O-(2,6-diamino-2,3,4,6-tetradeoxy-alpha-D-erythro-hexopyranosyl-(1-4))-2-deoxy-D-streptamine	ChEBI
O-3-Deoxy-4-C-methyl-3-(methylamino)-b-L-arabinopyranosyl-(1-6)-O-(2,6-diamino-2,3,4,6-tetradeoxy-a-D-erythro-hexopyranosyl-(1-4))-2-deoxy-D-streptamine	Generator
O-3-Deoxy-4-C-methyl-3-(methylamino)-β-L-arabinopyranosyl-(1-6)-O-(2,6-diamino-2,3,4,6-tetradeoxy-α-D-erythro-hexopyranosyl-(1-4))-2-deoxy-D-streptamine	Generator
Gentamicin C	MeSH
Gentamicin C1 sulfate	MeSH
Gentamicin C sulfate	MeSH
Gentamicin C1 sulfate (5:2)	MeSH
Gentamicin C2	MeSH
Gentamicin C1	MeSH
Gentamicin C2a	MeSH
Gentamicin C1a	ChEBI

Chemical Formula

C₁₉H₃₉N₅O₇

Average Mass

449.5423 Da

Monoisotopic Mass

449.28495 Da

IUPAC Name

(2R,3R,4R,5R)-2-{[(1S,2S,3R,4S,6R)-4,6-diamino-3-{[(2R,3R,6S)-3-amino-6-(aminomethyl)oxan-2-yl]oxy}-2-hydroxycyclohexyl]oxy}-5-methyl-4-(methylamino)oxane-3,5-diol

Traditional Name

gentamicin C1A

CAS Registry Number

Not Available

SMILES

[H]O[C@@]1([H])[C@@]([H])(O[C@]2([H])[C@@]([H])(O[H])[C@]([H])(O[C@@]3([H])O[C@]([H])(C([H])([H])N([H])[H])C([H])([H])C([H])([H])[C@@]3([H])N([H])[H])[C@@]([H])(N([H])[H])C([H])([H])[C@@]2([H])N([H])[H])OC([H])([H])[C@@](O[H])(C([H])([H])[H])[C@]1([H])N([H])C([H])([H])[H]

InChI Identifier

InChI=1S/C19H39N5O7/c1-19(27)7-28-18(13(26)16(19)24-2)31-15-11(23)5-10(22)14(12(15)25)30-17-9(21)4-3-8(6-20)29-17/h8-18,24-27H,3-7,20-23H2,1-2H3/t8-,9+,10-,11+,12-,13+,14+,15-,16+,17+,18+,19-/m0/s1

InChI Key

VEGXETMJINRLTH-BOZYPMBZSA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Apis cerana	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as aminocyclitol glycosides. These are organic compounds containing an amicocyclitol moiety glycosidically linked to a carbohydrate moiety. There are two major classes of aminoglycosides containing a 2-streptamine core. They are called 4,5- and 4,6-disubstituted 2-deoxystreptamines.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Aminocyclitol glycosides

Alternative Parents

Substituents

Amino cyclitol glycoside
2-deoxystreptamine aminoglycoside
Glycosyl compound
O-glycosyl compound
Aminocyclitol or derivatives
Cyclohexanol
Cyclohexylamine
Cyclitol or derivatives
Monosaccharide
Oxane
Tertiary alcohol
Cyclic alcohol
Secondary alcohol
1,2-aminoalcohol
Secondary amine
Acetal
Organoheterocyclic compound
Secondary aliphatic amine
Oxacycle
Alcohol
Hydrocarbon derivative
Primary aliphatic amine
Organopnictogen compound
Organic nitrogen compound
Amine
Primary amine
Organonitrogen compound
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

gentamycin C (CHEBI:27784 )

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	-4	ChemAxon
logS	-1.3	ALOGPS
pKa (Strongest Acidic)	12.55	ChemAxon
pKa (Strongest Basic)	9.9	ChemAxon
Physiological Charge	5	ChemAxon
Hydrogen Acceptor Count	12	ChemAxon
Hydrogen Donor Count	8	ChemAxon
Polar Surface Area	213.72 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	108.83 m³·mol⁻¹	ChemAxon
Polarizability	47.35 Å³	ChemAxon
Number of Rings	3	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

HMDB ID

Not Available

DrugBank ID

DB04729

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

65329

KEGG Compound ID

C00908

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

Not Available

PDB ID

Not Available

ChEBI ID

27784

Good Scents ID

Not Available

References

General References

Bhadani RV, Gajera HP, Hirpara DG, Kachhadiya HJ, Dave RA: Metabolomics of extracellular compounds and parasitic enzymes of Beauveria bassiana associated with biological control of whiteflies (Bemisia tabaci). Pestic Biochem Physiol. 2021 Jul;176:104877. doi: 10.1016/j.pestbp.2021.104877. Epub 2021 May 21. [PubMed:34119221 ]
Chen X, Zhang H, Zhou S, Bi M, Qi S, Gao H, Ni X, Xia H: The bifunctional enzyme, GenB4, catalyzes the last step of gentamicin 3',4'-di-deoxygenation via reduction and transamination activities. Microb Cell Fact. 2020 Mar 10;19(1):62. doi: 10.1186/s12934-020-01317-0. [PubMed:32156271 ]
Wei Z, Shi X, Lian R, Wang W, Hong W, Guo S: Exclusive Production of Gentamicin C1a from Micromonospora purpurea by Metabolic Engineering. Antibiotics (Basel). 2019 Dec 14;8(4). pii: antibiotics8040267. doi: 10.3390/antibiotics8040267. [PubMed:31847403 ]
Ishikawa M, Garcia-Mateo N, Cusak A, Lopez-Hernandez I, Fernandez-Martinez M, Muller M, Ruttiger L, Singer W, Lowenheim H, Kosec G, Fujs S, Martinez-Martinez L, Schimmang T, Petkovic H, Knipper M, Duran-Alonso MB: Lower ototoxicity and absence of hidden hearing loss point to gentamicin C1a and apramycin as promising antibiotics for clinical use. Sci Rep. 2019 Feb 20;9(1):2410. doi: 10.1038/s41598-019-38634-3. [PubMed:30787404 ]
Liu Y, Chang H, Li Z, Feng Y, Cheng D, Xue J: Biodegradation of gentamicin by bacterial consortia AMQD4 in synthetic medium and raw gentamicin sewage. Sci Rep. 2017 Sep 8;7(1):11004. doi: 10.1038/s41598-017-11529-x. [PubMed:28887556 ]
Yang B, Wang L, Luo C, Wang X, Sun C: Simultaneous Determination of 11 Aminoglycoside Residues in Honey, Milk, and Pork by Liquid Chromatography with Tandem Mass Spectrometry and Molecularly Imprinted Polymer Solid Phase Extraction. J AOAC Int. 2017 Nov 1;100(6):1869-1878. doi: 10.5740/jaoacint.16-0399. Epub 2017 Aug 8. [PubMed:28786377 ]
Wu Z, Gao W, Zhou S, Wen Z, Ni X, Xia H: Improving gentamicin B and gentamicin C1a production by engineering the glycosyltransferases that transfer primary metabolites into secondary metabolites biosynthesis. Microbiol Res. 2017 Oct;203:40-46. doi: 10.1016/j.micres.2017.06.006. Epub 2017 Jul 1. [PubMed:28754206 ]
Ni X, Zong T, Zhang H, Gu Y, Huang M, Tian W, Xia H: Biosynthesis of 3''-demethyl-gentamicin C components by genN disruption strain of Micromonospora echinospora and test their antimicrobial activities in vitro. Microbiol Res. 2016 Apr;185:36-44. doi: 10.1016/j.micres.2016.01.005. Epub 2016 Jan 28. [PubMed:26946376 ]
Gu Y, Ni X, Ren J, Gao H, Wang D, Xia H: Biosynthesis of Epimers C2 and C2a in the Gentamicin C Complex. Chembiochem. 2015 Sep 7;16(13):1933-1942. doi: 10.1002/cbic.201500258. Epub 2015 Jul 14. [PubMed:26083124 ]
Wang Y, Zhang Z, Wu L, Zhang X, Wang H, Ye W, Li P: Isolation and structure characterization of related impurities in etimicin intermediate P1 by LC/ESI-MS(n) and NMR. J Pharm Biomed Anal. 2014 Aug;97:97-102. doi: 10.1016/j.jpba.2014.04.024. Epub 2014 May 2. [PubMed:24858300 ]
Deubner, D., et al. (2003). Deubner, D., et al, Magn. Reson. Chem. 41, 589 (2003). Mag. Reson. Chem..

Showing NP-Card for gentamicin C1a (NP0030291)

MOL for NP0030291 (gentamicin C1a)

3D MOL for NP0030291 (gentamicin C1a)

3D SDF for NP0030291 (gentamicin C1a)

3D-SDF for NP0030291 (gentamicin C1a)

PDB for NP0030291 (gentamicin C1a)

3D PDB for NP0030291 (gentamicin C1a)

SMILES for NP0030291 (gentamicin C1a)

INCHI for NP0030291 (gentamicin C1a)

Structure for NP0030291 (gentamicin C1a)

3D Structure for NP0030291 (gentamicin C1a)