NP-MRD: Showing NP-Card for Amatyemide A (NP0350546)

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Record Information

Version

2.0

Created at

2024-12-13 06:45:29 UTC

Updated at

2025-06-11 06:35:05 UTC

NP-MRD ID

NP0350546

Natural Product DOI

https://doi.org/10.57994/3520

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Amatyemide A

Description

Based on a literature review very few articles have been published on Amatyemide A.

Structure

MOL SDF PDB SMILES InChI


  Mrv2104 03122306552D          

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M  END


  Mrv2104 03122306552D          

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 66 67  2  0  0  0  0
 62 68  2  0  0  0  0
 55 69  2  0  0  0  0
 48 70  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0350546

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CCCCCCCCCC[C@H]1OC(=O)[C@H](CC(C)C)N(C)C(=O)[C@@H](NC(=O)[C@@H](CC2=CC=CC=C2)NC(=O)[C@@H](OC(=O)[C@@H](NC(=O)[C@H](C)NC(=O)[C@H](CC(C)C)NC1=O)[C@@H](C)OC)[C@@H](C)CC)C(C)C

> <INCHI_IDENTIFIER>
InChI=1S/C53H88N6O11/c1-14-16-17-18-19-20-21-25-28-42-49(63)55-39(29-32(3)4)47(61)54-36(10)46(60)58-44(37(11)68-13)53(67)70-45(35(9)15-2)50(64)56-40(31-38-26-23-22-24-27-38)48(62)57-43(34(7)8)51(65)59(12)41(30-33(5)6)52(66)69-42/h22-24,26-27,32-37,39-45H,14-21,25,28-31H2,1-13H3,(H,54,61)(H,55,63)(H,56,64)(H,57,62)(H,58,60)/t35-,36-,37+,39-,40+,41-,42+,43-,44-,45-/m0/s1

> <INCHI_KEY>
LWKYQYARPNWMSC-NQIWARSRSA-N

> <FORMULA>
C53H88N6O11

> <MOLECULAR_WEIGHT>
985.318

> <EXACT_MASS>
984.651107678

> <JCHEM_ACCEPTOR_COUNT>
9

> <JCHEM_ATOM_COUNT>
158

> <JCHEM_AVERAGE_POLARIZABILITY>
110.19028789178819

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3S,6S,9R,12S,15S,18S,21S,24R)-9-benzyl-12-[(2S)-butan-2-yl]-24-decyl-15-[(1R)-1-methoxyethyl]-4,18-dimethyl-3,21-bis(2-methylpropyl)-6-(propan-2-yl)-1,13-dioxa-4,7,10,16,19,22-hexaazacyclotetracosan-2,5,8,11,14,17,20,23-octone

> <JCHEM_LOGP>
7.865814359666668

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
11.888896621520665

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.444680260089136

> <JCHEM_PKA_STRONGEST_BASIC>
-3.1470434331337915

> <JCHEM_POLAR_SURFACE_AREA>
227.64

> <JCHEM_REFRACTIVITY>
265.9804000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
20

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
(3S,6S,9R,12S,15S,18S,21S,24R)-9-benzyl-12-[(2S)-butan-2-yl]-24-decyl-6-isopropyl-15-[(1R)-1-methoxyethyl]-4,18-dimethyl-3,21-bis(2-methylpropyl)-1,13-dioxa-4,7,10,16,19,22-hexaazacyclotetracosan-2,5,8,11,14,17,20,23-octone

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 12-MAR-23   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   12-MAR-23         0                                  
HETATM    1  O   UNK     0      -6.300  -9.679   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0      -5.901  -8.192   0.000  0.00  0.00           C+0
HETATM    3  N   UNK     0      -4.414  -7.793   0.000  0.00  0.00           N+0
HETATM    4  C   UNK     0      -3.644  -9.127   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -4.414 -10.460   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -3.644 -11.794   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -5.954 -10.460   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -2.104  -9.127   0.000  0.00  0.00           C+0
HETATM    9  N   UNK     0      -1.334  -7.793   0.000  0.00  0.00           N+0
HETATM   10  C   UNK     0      -1.923  -6.370   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       0.154  -8.192   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       0.552  -9.679   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       2.040 -10.078   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       3.129  -8.989   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       2.439 -11.565   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       1.243  -7.103   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0       0.844  -5.615   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0       2.178  -4.845   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       2.178  -3.305   0.000  0.00  0.00           C+0
HETATM   20  N   UNK     0       0.844  -2.535   0.000  0.00  0.00           N+0
HETATM   21  C   UNK     0       1.243  -1.048   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       2.730  -0.649   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       3.129   0.838   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       2.040   1.927   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       4.616   1.237   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0       3.512  -2.535   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0       3.512  -5.615   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       4.845  -4.845   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       6.179  -5.615   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       7.513  -4.845   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       8.846  -5.615   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      10.180  -4.845   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      11.514  -5.615   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0      12.847  -4.845   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0      14.181  -5.615   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0      14.181  -7.155   0.000  0.00  0.00           C+0
HETATM   37  O   UNK     0       2.730  -7.501   0.000  0.00  0.00           O+0
HETATM   38  O   UNK     0      -1.334 -10.460   0.000  0.00  0.00           O+0
HETATM   39  C   UNK     0      -6.990  -7.103   0.000  0.00  0.00           C+0
HETATM   40  C   UNK     0      -8.478  -7.501   0.000  0.00  0.00           C+0
HETATM   41  C   UNK     0      -8.876  -8.989   0.000  0.00  0.00           C+0
HETATM   42  C   UNK     0      -7.787 -10.078   0.000  0.00  0.00           C+0
HETATM   43  C   UNK     0      -8.186 -11.565   0.000  0.00  0.00           C+0
HETATM   44  C   UNK     0      -9.673 -11.964   0.000  0.00  0.00           C+0
HETATM   45  C   UNK     0     -10.762 -10.875   0.000  0.00  0.00           C+0
HETATM   46  C   UNK     0     -10.364  -9.387   0.000  0.00  0.00           C+0
HETATM   47  N   UNK     0      -6.592  -5.615   0.000  0.00  0.00           N+0
HETATM   48  C   UNK     0      -7.925  -4.845   0.000  0.00  0.00           C+0
HETATM   49  C   UNK     0      -7.925  -3.305   0.000  0.00  0.00           C+0
HETATM   50  C   UNK     0      -9.259  -2.535   0.000  0.00  0.00           C+0
HETATM   51  C   UNK     0     -10.593  -3.305   0.000  0.00  0.00           C+0
HETATM   52  C   UNK     0      -9.259  -0.995   0.000  0.00  0.00           C+0
HETATM   53  C   UNK     0     -10.593  -0.225   0.000  0.00  0.00           C+0
HETATM   54  O   UNK     0      -6.592  -2.535   0.000  0.00  0.00           O+0
HETATM   55  C   UNK     0      -6.990  -1.048   0.000  0.00  0.00           C+0
HETATM   56  C   UNK     0      -5.901   0.041   0.000  0.00  0.00           C+0
HETATM   57  C   UNK     0      -6.300   1.529   0.000  0.00  0.00           C+0
HETATM   58  O   UNK     0      -7.787   1.927   0.000  0.00  0.00           O+0
HETATM   59  C   UNK     0      -8.186   3.415   0.000  0.00  0.00           C+0
HETATM   60  C   UNK     0      -5.211   2.618   0.000  0.00  0.00           C+0
HETATM   61  N   UNK     0      -4.414  -0.357   0.000  0.00  0.00           N+0
HETATM   62  C   UNK     0      -3.644   0.976   0.000  0.00  0.00           C+0
HETATM   63  C   UNK     0      -2.104   0.976   0.000  0.00  0.00           C+0
HETATM   64  C   UNK     0      -1.334   2.310   0.000  0.00  0.00           C+0
HETATM   65  N   UNK     0      -1.334  -0.357   0.000  0.00  0.00           N+0
HETATM   66  C   UNK     0       0.154   0.041   0.000  0.00  0.00           C+0
HETATM   67  O   UNK     0       0.552   1.529   0.000  0.00  0.00           O+0
HETATM   68  O   UNK     0      -4.414   2.310   0.000  0.00  0.00           O+0
HETATM   69  O   UNK     0      -8.478  -0.649   0.000  0.00  0.00           O+0
HETATM   70  O   UNK     0      -9.259  -5.615   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   39                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5    8                                                  
CONECT    5    4    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5                                                            
CONECT    8    4    9   38                                                  
CONECT    9    8   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9   12   16                                                  
CONECT   12   11   13                                                       
CONECT   13   12   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13                                                            
CONECT   16   11   17   37                                                  
CONECT   17   16   18                                                       
CONECT   18   17   19   27                                                  
CONECT   19   18   20   26                                                  
CONECT   20   19   21                                                       
CONECT   21   20   22   66                                                  
CONECT   22   21   23                                                       
CONECT   23   22   24   25                                                  
CONECT   24   23                                                            
CONECT   25   23                                                            
CONECT   26   19                                                            
CONECT   27   18   28                                                       
CONECT   28   27   29                                                       
CONECT   29   28   30                                                       
CONECT   30   29   31                                                       
CONECT   31   30   32                                                       
CONECT   32   31   33                                                       
CONECT   33   32   34                                                       
CONECT   34   33   35                                                       
CONECT   35   34   36                                                       
CONECT   36   35                                                            
CONECT   37   16                                                            
CONECT   38    8                                                            
CONECT   39    2   40   47                                                  
CONECT   40   39   41                                                       
CONECT   41   40   42   46                                                  
CONECT   42   41   43                                                       
CONECT   43   42   44                                                       
CONECT   44   43   45                                                       
CONECT   45   44   46                                                       
CONECT   46   45   41                                                       
CONECT   47   39   48                                                       
CONECT   48   47   49   70                                                  
CONECT   49   48   50   54                                                  
CONECT   50   49   51   52                                                  
CONECT   51   50                                                            
CONECT   52   50   53                                                       
CONECT   53   52                                                            
CONECT   54   49   55                                                       
CONECT   55   54   56   69                                                  
CONECT   56   55   57   61                                                  
CONECT   57   56   58   60                                                  
CONECT   58   57   59                                                       
CONECT   59   58                                                            
CONECT   60   57                                                            
CONECT   61   56   62                                                       
CONECT   62   61   63   68                                                  
CONECT   63   62   64   65                                                  
CONECT   64   63                                                            
CONECT   65   63   66                                                       
CONECT   66   65   21   67                                                  
CONECT   67   66                                                            
CONECT   68   62                                                            
CONECT   69   55                                                            
CONECT   70   48                                                            
MASTER        0    0    0    0    0    0    0    0   70    0  142    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₅₃H₈₈N₆O₁₁

Average Mass

985.3180 Da

Monoisotopic Mass

984.65111 Da

IUPAC Name

(3S,6S,9R,12S,15S,18S,21S,24R)-9-benzyl-12-[(2S)-butan-2-yl]-24-decyl-15-[(1R)-1-methoxyethyl]-4,18-dimethyl-3,21-bis(2-methylpropyl)-6-(propan-2-yl)-1,13-dioxa-4,7,10,16,19,22-hexaazacyclotetracosan-2,5,8,11,14,17,20,23-octone

Traditional Name

(3S,6S,9R,12S,15S,18S,21S,24R)-9-benzyl-12-[(2S)-butan-2-yl]-24-decyl-6-isopropyl-15-[(1R)-1-methoxyethyl]-4,18-dimethyl-3,21-bis(2-methylpropyl)-1,13-dioxa-4,7,10,16,19,22-hexaazacyclotetracosan-2,5,8,11,14,17,20,23-octone

CAS Registry Number

Not Available

SMILES

CCCCCCCCCC[C@H]1OC(=O)[C@H](CC(C)C)N(C)C(=O)[C@@H](NC(=O)[C@@H](CC2=CC=CC=C2)NC(=O)[C@@H](OC(=O)[C@@H](NC(=O)[C@H](C)NC(=O)[C@H](CC(C)C)NC1=O)[C@@H](C)OC)[C@@H](C)CC)C(C)C

InChI Identifier

InChI=1S/C53H88N6O11/c1-14-16-17-18-19-20-21-25-28-42-49(63)55-39(29-32(3)4)47(61)54-36(10)46(60)58-44(37(11)68-13)53(67)70-45(35(9)15-2)50(64)56-40(31-38-26-23-22-24-27-38)48(62)57-43(34(7)8)51(65)59(12)41(30-33(5)6)52(66)69-42/h22-24,26-27,32-37,39-45H,14-21,25,28-31H2,1-13H3,(H,54,61)(H,55,63)(H,56,64)(H,57,62)(H,58,60)/t35-,36-,37+,39-,40+,41-,42+,43-,44-,45-/m0/s1

InChI Key

LWKYQYARPNWMSC-NQIWARSRSA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
ROESY NMR	[¹H, ¹H] NMR Spectrum (2D, 800 MHz, CDCl3, experimental)	yux@oregonstate.edu	Not Available	Not Available	2024-12-13	View Spectrum
HSQC NMR	[¹H, ¹³C] NMR Spectrum (2D, 800 MHz, CDCl3, experimental)	yux@oregonstate.edu	Not Available	Not Available	2024-12-13	View Spectrum
COSY NMR	[¹H, ¹H] NMR Spectrum (2D, 800 MHz, CDCl3, experimental)	yux@oregonstate.edu	Not Available	Not Available	2024-12-13	View Spectrum
HMBC NMR	[¹H, ¹³C] NMR Spectrum (2D, 800 MHz, CDCl3, experimental)	yux@oregonstate.edu	Not Available	Not Available	2024-12-13	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, CDCl3, experimental)	yux@oregonstate.edu	Not Available	Not Available	2024-12-13	View Spectrum

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View

Chemical Shift Submissions

Not Available

Species

Species of Origin

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	7.87	ChemAxon
pKa (Strongest Acidic)	11.44	ChemAxon
pKa (Strongest Basic)	-3.1	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	9	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	227.64 Å²	ChemAxon
Rotatable Bond Count	20	ChemAxon
Refractivity	265.98 m³·mol⁻¹	ChemAxon
Polarizability	110.19 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

Not Available

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Showing NP-Card for Amatyemide A (NP0350546)

MOL for NP0350546 (Amatyemide A)

3D MOL for NP0350546 (Amatyemide A)

3D SDF for NP0350546 (Amatyemide A)

3D-SDF for NP0350546 (Amatyemide A)

PDB for NP0350546 (Amatyemide A)

3D PDB for NP0350546 (Amatyemide A)

SMILES for NP0350546 (Amatyemide A)

INCHI for NP0350546 (Amatyemide A)

Structure for NP0350546 (Amatyemide A)

3D Structure for NP0350546 (Amatyemide A)