NP-MRD: Showing NP-Card for Nocardimicin J (NP0341997)

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Record Information

Version

2.0

Created at

2024-11-29 06:45:14 UTC

Updated at

2024-11-29 08:00:51 UTC

NP-MRD ID

NP0341997

Natural Product DOI

https://doi.org/10.57994/3490

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Nocardimicin J

Description

Based on a literature review very few articles have been published on Nocardimicin J.

Structure

MOL SDF PDB SMILES InChI


  Mrv2104 02262306552D          

 55 57  0  0  1  0            999 V2000
    2.2128   -9.5325    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9964   -9.7904    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6116   -9.2406    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4431   -8.4330    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6907   -8.0946    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.7801   -7.2745    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1691   -6.7201    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3436   -5.9138    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.7326   -5.3595    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.9471   -5.6114    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    5.6605   -4.0996    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4461   -3.8476    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    7.8427   -4.1500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.4537   -4.7043    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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  1  2  1  0  0  0  0
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 34 35  1  1  0  0  0
 34 36  1  0  0  0  0
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 38 37  1  6  0  0  0
 38 39  1  0  0  0  0
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 36 47  2  0  0  0  0
 20 48  2  0  0  0  0
  7 49  2  0  0  0  0
  6 50  2  0  0  0  0
 50 51  1  0  0  0  0
  4 51  1  0  0  0  0
  3 52  1  0  0  0  0
 52 53  2  0  0  0  0
 53 54  1  0  0  0  0
 54 55  2  0  0  0  0
  2 55  1  0  0  0  0
M  END


  Mrv2104 02262306552D          

 55 57  0  0  1  0            999 V2000
    2.2128   -9.5325    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9964   -9.7904    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    2.6928   -4.3012    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3835   -6.9721    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5877   -7.1060    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    3.9486  -10.8559    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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  1  2  1  0  0  0  0
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 38 45  1  0  0  0  0
 45 46  2  0  0  0  0
 36 47  2  0  0  0  0
 20 48  2  0  0  0  0
  7 49  2  0  0  0  0
  6 50  2  0  0  0  0
 50 51  1  0  0  0  0
  4 51  1  0  0  0  0
  3 52  1  0  0  0  0
 52 53  2  0  0  0  0
 53 54  1  0  0  0  0
 54 55  2  0  0  0  0
  2 55  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0341997

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CCCCCCCCCCC[C@H](OC(=O)[C@H](CCCCN(O)C(=O)CC)NC(=O)C1=COC(=N1)C1=C(O)C=CC=C1)[C@@H](C)C(=O)N[C@@H]1CCCCN(O)C1=O

> <INCHI_IDENTIFIER>
InChI=1S/C40H61N5O10/c1-4-6-7-8-9-10-11-12-13-24-34(28(3)36(48)41-30-21-16-19-26-45(53)39(30)50)55-40(51)31(22-17-18-25-44(52)35(47)5-2)42-37(49)32-27-54-38(43-32)29-20-14-15-23-33(29)46/h14-15,20,23,27-28,30-31,34,46,52-53H,4-13,16-19,21-22,24-26H2,1-3H3,(H,41,48)(H,42,49)/t28-,30-,31+,34+/m1/s1

> <INCHI_KEY>
GIZWVQWDRIXUEK-LSJVWSNHSA-N

> <FORMULA>
C40H61N5O10

> <MOLECULAR_WEIGHT>
771.953

> <EXACT_MASS>
771.441843184

> <JCHEM_ACCEPTOR_COUNT>
9

> <JCHEM_ATOM_COUNT>
116

> <JCHEM_AVERAGE_POLARIZABILITY>
85.51973465319819

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1R,2S)-1-{[(3R)-1-hydroxy-2-oxoazepan-3-yl]carbamoyl}-1-methyltridecan-2-yl (2S)-2-{[2-(2-hydroxyphenyl)-1,3-oxazol-4-yl]formamido}-6-(N-hydroxypropanamido)hexanoate

> <JCHEM_LOGP>
6.242239086999998

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
8.380071189078295

> <JCHEM_PKA_STRONGEST_ACIDIC>
7.8938960743486914

> <JCHEM_PKA_STRONGEST_BASIC>
-1.3882175010528321

> <JCHEM_POLAR_SURFACE_AREA>
211.83999999999997

> <JCHEM_REFRACTIVITY>
214.83270000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
25

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
(1R,2S)-1-{[(3R)-1-hydroxy-2-oxoazepan-3-yl]carbamoyl}-1-methyltridecan-2-yl (2S)-2-{[2-(2-hydroxyphenyl)-1,3-oxazol-4-yl]formamido}-6-(N-hydroxypropanamido)hexanoate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 26-FEB-23   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   26-FEB-23         0                                  
HETATM    1  O   UNK     0       4.131 -17.794   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       5.593 -18.275   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       6.742 -17.249   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       6.427 -15.742   0.000  0.00  0.00           C+0
HETATM    5  N   UNK     0       5.023 -15.110   0.000  0.00  0.00           N+0
HETATM    6  C   UNK     0       5.189 -13.579   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       4.049 -12.544   0.000  0.00  0.00           C+0
HETATM    8  N   UNK     0       4.375 -11.039   0.000  0.00  0.00           N+0
HETATM    9  C   UNK     0       3.234 -10.004   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       1.768 -10.475   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       0.627  -9.440   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -0.839  -9.910   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -1.980  -8.875   0.000  0.00  0.00           C+0
HETATM   14  N   UNK     0      -3.446  -9.346   0.000  0.00  0.00           N+0
HETATM   15  O   UNK     0      -3.772 -10.851   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0      -4.587  -8.311   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      -6.053  -8.781   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      -7.194  -7.747   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0      -4.261  -6.806   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0       3.560  -8.499   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0       2.420  -7.464   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0       2.745  -5.959   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       4.212  -5.489   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       5.352  -6.524   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       6.819  -6.053   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       7.959  -7.088   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       9.426  -6.618   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      10.566  -7.653   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      12.033  -7.182   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      13.173  -8.217   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      14.640  -7.747   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      15.780  -8.781   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      15.454 -10.287   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       1.605  -4.925   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0       0.138  -5.395   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0       1.931  -3.419   0.000  0.00  0.00           C+0
HETATM   37  N   UNK     0       0.790  -2.385   0.000  0.00  0.00           N+0
HETATM   38  C   UNK     0       1.116  -0.880   0.000  0.00  0.00           C+0
HETATM   39  C   UNK     0      -0.099   0.067   0.000  0.00  0.00           C+0
HETATM   40  C   UNK     0      -0.116   1.607   0.000  0.00  0.00           C+0
HETATM   41  C   UNK     0       1.077   2.581   0.000  0.00  0.00           C+0
HETATM   42  C   UNK     0       2.583   2.255   0.000  0.00  0.00           C+0
HETATM   43  N   UNK     0       3.266   0.875   0.000  0.00  0.00           N+0
HETATM   44  O   UNK     0       4.806   0.892   0.000  0.00  0.00           O+0
HETATM   45  C   UNK     0       2.614  -0.520   0.000  0.00  0.00           C+0
HETATM   46  O   UNK     0       3.587  -1.713   0.000  0.00  0.00           O+0
HETATM   47  O   UNK     0       3.397  -2.949   0.000  0.00  0.00           O+0
HETATM   48  O   UNK     0       5.027  -8.029   0.000  0.00  0.00           O+0
HETATM   49  O   UNK     0       2.583 -13.015   0.000  0.00  0.00           O+0
HETATM   50  C   UNK     0       6.697 -13.265   0.000  0.00  0.00           C+0
HETATM   51  O   UNK     0       7.462 -14.601   0.000  0.00  0.00           O+0
HETATM   52  C   UNK     0       8.205 -17.731   0.000  0.00  0.00           C+0
HETATM   53  C   UNK     0       8.519 -19.238   0.000  0.00  0.00           C+0
HETATM   54  C   UNK     0       7.371 -20.264   0.000  0.00  0.00           C+0
HETATM   55  C   UNK     0       5.908 -19.783   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3   55                                                  
CONECT    3    2    4   52                                                  
CONECT    4    3    5   51                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7   50                                                  
CONECT    7    6    8   49                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10   20                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15   16                                                  
CONECT   15   14                                                            
CONECT   16   14   17   19                                                  
CONECT   17   16   18                                                       
CONECT   18   17                                                            
CONECT   19   16                                                            
CONECT   20    9   21   48                                                  
CONECT   21   20   22                                                       
CONECT   22   21   23   34                                                  
CONECT   23   22   24                                                       
CONECT   24   23   25                                                       
CONECT   25   24   26                                                       
CONECT   26   25   27                                                       
CONECT   27   26   28                                                       
CONECT   28   27   29                                                       
CONECT   29   28   30                                                       
CONECT   30   29   31                                                       
CONECT   31   30   32                                                       
CONECT   32   31   33                                                       
CONECT   33   32                                                            
CONECT   34   22   35   36                                                  
CONECT   35   34                                                            
CONECT   36   34   37   47                                                  
CONECT   37   36   38                                                       
CONECT   38   37   39   45                                                  
CONECT   39   38   40                                                       
CONECT   40   39   41                                                       
CONECT   41   40   42                                                       
CONECT   42   41   43                                                       
CONECT   43   42   44   45                                                  
CONECT   44   43                                                            
CONECT   45   43   38   46                                                  
CONECT   46   45                                                            
CONECT   47   36                                                            
CONECT   48   20                                                            
CONECT   49    7                                                            
CONECT   50    6   51                                                       
CONECT   51   50    4                                                       
CONECT   52    3   53                                                       
CONECT   53   52   54                                                       
CONECT   54   53   55                                                       
CONECT   55   54    2                                                       
MASTER        0    0    0    0    0    0    0    0   55    0  114    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₄₀H₆₁N₅O₁₀

Average Mass

771.9530 Da

Monoisotopic Mass

771.44184 Da

IUPAC Name

(1R,2S)-1-{[(3R)-1-hydroxy-2-oxoazepan-3-yl]carbamoyl}-1-methyltridecan-2-yl (2S)-2-{[2-(2-hydroxyphenyl)-1,3-oxazol-4-yl]formamido}-6-(N-hydroxypropanamido)hexanoate

Traditional Name

(1R,2S)-1-{[(3R)-1-hydroxy-2-oxoazepan-3-yl]carbamoyl}-1-methyltridecan-2-yl (2S)-2-{[2-(2-hydroxyphenyl)-1,3-oxazol-4-yl]formamido}-6-(N-hydroxypropanamido)hexanoate

CAS Registry Number

Not Available

SMILES

CCCCCCCCCCC[C@H](OC(=O)[C@H](CCCCN(O)C(=O)CC)NC(=O)C1=COC(=N1)C1=C(O)C=CC=C1)[C@@H](C)C(=O)N[C@@H]1CCCCN(O)C1=O

InChI Identifier

InChI=1S/C40H61N5O10/c1-4-6-7-8-9-10-11-12-13-24-34(28(3)36(48)41-30-21-16-19-26-45(53)39(30)50)55-40(51)31(22-17-18-25-44(52)35(47)5-2)42-37(49)32-27-54-38(43-32)29-20-14-15-23-33(29)46/h14-15,20,23,27-28,30-31,34,46,52-53H,4-13,16-19,21-22,24-26H2,1-3H3,(H,41,48)(H,42,49)/t28-,30-,31+,34+/m1/s1

InChI Key

GIZWVQWDRIXUEK-LSJVWSNHSA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
HSQC NMR	[¹H, ¹³C] NMR Spectrum (2D, 600 MHz, C2D6OS, experimental)	1584281463@qq.com	Ocean University of China	Suling Xu	2024-11-29	View Spectrum
NOESY NMR	[¹H, ¹H] NMR Spectrum (2D, 600 MHz, C2D6OS, experimental)	1584281463@qq.com	Ocean University of China	Suling Xu	2024-11-29	View Spectrum
HMBC NMR	[¹H, ¹³C] NMR Spectrum (2D, 600 MHz, C2D6OS, experimental)	1584281463@qq.com	Ocean University of China	Suling Xu	2024-11-29	View Spectrum
HETLOC NMR	[¹H, ¹H] NMR Spectrum (2D, 600 MHz, C2D6OS, experimental)	1584281463@qq.com	Ocean University of China	Suling Xu	2024-11-29	View Spectrum
COSY NMR	[¹H, ¹H] NMR Spectrum (2D, 600 MHz, C2D6OS, experimental)	1584281463@qq.com	Ocean University of China	Suling Xu	2024-11-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, C2D6OS, experimental)	1584281463@qq.com	Ocean University of China	Suling Xu	2024-11-29	View Spectrum
DEPT NMR	¹³C NMR Spectrum (1D, 151 MHz, C2D6OS, experimental)	1584281463@qq.com	Ocean University of China	Suling Xu	2024-11-29	View Spectrum

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
sp		Not Available

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	6.24	ChemAxon
pKa (Strongest Acidic)	7.89	ChemAxon
pKa (Strongest Basic)	-1.4	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	9	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	211.84 Å²	ChemAxon
Rotatable Bond Count	25	ChemAxon
Refractivity	214.83 m³·mol⁻¹	ChemAxon
Polarizability	85.52 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

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

Not Available

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Nocardimicin J (NP0341997)

MOL for NP0341997 (Nocardimicin J)

3D MOL for NP0341997 (Nocardimicin J)

3D SDF for NP0341997 (Nocardimicin J)

3D-SDF for NP0341997 (Nocardimicin J)

PDB for NP0341997 (Nocardimicin J)

3D PDB for NP0341997 (Nocardimicin J)

SMILES for NP0341997 (Nocardimicin J)

INCHI for NP0341997 (Nocardimicin J)

Structure for NP0341997 (Nocardimicin J)

3D Structure for NP0341997 (Nocardimicin J)