NP-MRD: Showing NP-Card for [S-Hda]-amatyemide B (NP0350549)

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Record Information

Version

2.0

Created at

2024-12-13 06:54:14 UTC

Updated at

2025-06-11 06:35:08 UTC

NP-MRD ID

NP0350549

Natural Product DOI

https://doi.org/10.57994/3523

Secondary Accession Numbers

None

Natural Product Identification

Common Name

[S-Hda]-amatyemide B

Description

Based on a literature review very few articles have been published on [S-Hda]-amatyemide B.

Structure

MOL SDF PDB SMILES InChI


  Mrv2104 03122307032D          

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M  END


  Mrv2104 03122307032D          

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M  END
> <DATABASE_ID>
NP0350549

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CCCCCCCC[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/C51H84N6O11/c1-14-16-17-18-19-23-26-40-47(61)53-37(27-30(3)4)45(59)52-34(10)44(58)56-42(35(11)66-13)51(65)68-43(33(9)15-2)48(62)54-38(29-36-24-21-20-22-25-36)46(60)55-41(32(7)8)49(63)57(12)39(28-31(5)6)50(64)67-40/h20-22,24-25,30-35,37-43H,14-19,23,26-29H2,1-13H3,(H,52,59)(H,53,61)(H,54,62)(H,55,60)(H,56,58)/t33-,34-,35+,37-,38+,39-,40-,41-,42-,43-/m0/s1

> <INCHI_KEY>
YCHHXEOVQGRFMK-GIKUMCPCSA-N

> <FORMULA>
C51H84N6O11

> <MOLECULAR_WEIGHT>
957.264

> <EXACT_MASS>
956.619807549

> <JCHEM_ACCEPTOR_COUNT>
9

> <JCHEM_ATOM_COUNT>
152

> <JCHEM_AVERAGE_POLARIZABILITY>
104.3959139603196

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3S,6S,9R,12S,15S,18S,21S,24S)-9-benzyl-12-[(2S)-butan-2-yl]-15-[(1R)-1-methoxyethyl]-4,18-dimethyl-3,21-bis(2-methylpropyl)-24-octyl-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>
6.976677029666668

> <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>
256.7784000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
18

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
(3S,6S,9R,12S,15S,18S,21S,24S)-9-benzyl-12-[(2S)-butan-2-yl]-6-isopropyl-15-[(1R)-1-methoxyethyl]-4,18-dimethyl-3,21-bis(2-methylpropyl)-24-octyl-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      11.514  -7.155   0.000  0.00  0.00           C+0
HETATM   35  O   UNK     0       2.730  -7.501   0.000  0.00  0.00           O+0
HETATM   36  O   UNK     0      -1.334 -10.460   0.000  0.00  0.00           O+0
HETATM   37  C   UNK     0      -6.990  -7.103   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0      -8.478  -7.501   0.000  0.00  0.00           C+0
HETATM   39  C   UNK     0      -8.876  -8.989   0.000  0.00  0.00           C+0
HETATM   40  C   UNK     0      -7.787 -10.078   0.000  0.00  0.00           C+0
HETATM   41  C   UNK     0      -8.186 -11.565   0.000  0.00  0.00           C+0
HETATM   42  C   UNK     0      -9.673 -11.964   0.000  0.00  0.00           C+0
HETATM   43  C   UNK     0     -10.762 -10.875   0.000  0.00  0.00           C+0
HETATM   44  C   UNK     0     -10.364  -9.387   0.000  0.00  0.00           C+0
HETATM   45  N   UNK     0      -6.592  -5.615   0.000  0.00  0.00           N+0
HETATM   46  C   UNK     0      -7.925  -4.845   0.000  0.00  0.00           C+0
HETATM   47  C   UNK     0      -7.925  -3.305   0.000  0.00  0.00           C+0
HETATM   48  C   UNK     0      -9.259  -2.535   0.000  0.00  0.00           C+0
HETATM   49  C   UNK     0     -10.593  -3.305   0.000  0.00  0.00           C+0
HETATM   50  C   UNK     0      -9.259  -0.995   0.000  0.00  0.00           C+0
HETATM   51  C   UNK     0     -10.593  -0.225   0.000  0.00  0.00           C+0
HETATM   52  O   UNK     0      -6.592  -2.535   0.000  0.00  0.00           O+0
HETATM   53  C   UNK     0      -6.990  -1.048   0.000  0.00  0.00           C+0
HETATM   54  C   UNK     0      -5.901   0.041   0.000  0.00  0.00           C+0
HETATM   55  C   UNK     0      -6.300   1.529   0.000  0.00  0.00           C+0
HETATM   56  O   UNK     0      -7.787   1.927   0.000  0.00  0.00           O+0
HETATM   57  C   UNK     0      -8.186   3.415   0.000  0.00  0.00           C+0
HETATM   58  C   UNK     0      -5.211   2.618   0.000  0.00  0.00           C+0
HETATM   59  N   UNK     0      -4.414  -0.357   0.000  0.00  0.00           N+0
HETATM   60  C   UNK     0      -3.644   0.976   0.000  0.00  0.00           C+0
HETATM   61  C   UNK     0      -2.104   0.976   0.000  0.00  0.00           C+0
HETATM   62  C   UNK     0      -1.334   2.310   0.000  0.00  0.00           C+0
HETATM   63  N   UNK     0      -1.334  -0.357   0.000  0.00  0.00           N+0
HETATM   64  C   UNK     0       0.154   0.041   0.000  0.00  0.00           C+0
HETATM   65  O   UNK     0       0.552   1.529   0.000  0.00  0.00           O+0
HETATM   66  O   UNK     0      -4.414   2.310   0.000  0.00  0.00           O+0
HETATM   67  O   UNK     0      -8.478  -0.649   0.000  0.00  0.00           O+0
HETATM   68  O   UNK     0      -9.259  -5.615   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   37                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5    8                                                  
CONECT    5    4    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5                                                            
CONECT    8    4    9   36                                                  
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   35                                                  
CONECT   17   16   18                                                       
CONECT   18   17   19   27                                                  
CONECT   19   18   20   26                                                  
CONECT   20   19   21                                                       
CONECT   21   20   22   64                                                  
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                                                            
CONECT   35   16                                                            
CONECT   36    8                                                            
CONECT   37    2   38   45                                                  
CONECT   38   37   39                                                       
CONECT   39   38   40   44                                                  
CONECT   40   39   41                                                       
CONECT   41   40   42                                                       
CONECT   42   41   43                                                       
CONECT   43   42   44                                                       
CONECT   44   43   39                                                       
CONECT   45   37   46                                                       
CONECT   46   45   47   68                                                  
CONECT   47   46   48   52                                                  
CONECT   48   47   49   50                                                  
CONECT   49   48                                                            
CONECT   50   48   51                                                       
CONECT   51   50                                                            
CONECT   52   47   53                                                       
CONECT   53   52   54   67                                                  
CONECT   54   53   55   59                                                  
CONECT   55   54   56   58                                                  
CONECT   56   55   57                                                       
CONECT   57   56                                                            
CONECT   58   55                                                            
CONECT   59   54   60                                                       
CONECT   60   59   61   66                                                  
CONECT   61   60   62   63                                                  
CONECT   62   61                                                            
CONECT   63   61   64                                                       
CONECT   64   63   21   65                                                  
CONECT   65   64                                                            
CONECT   66   60                                                            
CONECT   67   53                                                            
CONECT   68   46                                                            
MASTER        0    0    0    0    0    0    0    0   68    0  138    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₅₁H₈₄N₆O₁₁

Average Mass

957.2640 Da

Monoisotopic Mass

956.61981 Da

IUPAC Name

(3S,6S,9R,12S,15S,18S,21S,24S)-9-benzyl-12-[(2S)-butan-2-yl]-15-[(1R)-1-methoxyethyl]-4,18-dimethyl-3,21-bis(2-methylpropyl)-24-octyl-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,24S)-9-benzyl-12-[(2S)-butan-2-yl]-6-isopropyl-15-[(1R)-1-methoxyethyl]-4,18-dimethyl-3,21-bis(2-methylpropyl)-24-octyl-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

CCCCCCCC[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/C51H84N6O11/c1-14-16-17-18-19-23-26-40-47(61)53-37(27-30(3)4)45(59)52-34(10)44(58)56-42(35(11)66-13)51(65)68-43(33(9)15-2)48(62)54-38(29-36-24-21-20-22-25-36)46(60)55-41(32(7)8)49(63)57(12)39(28-31(5)6)50(64)67-40/h20-22,24-25,30-35,37-43H,14-19,23,26-29H2,1-13H3,(H,52,59)(H,53,61)(H,54,62)(H,55,60)(H,56,58)/t33-,34-,35+,37-,38+,39-,40-,41-,42-,43-/m0/s1

InChI Key

YCHHXEOVQGRFMK-GIKUMCPCSA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
COSY NMR	[¹H, ¹H] NMR Spectrum (2D, 700 MHz, CDCl3, experimental)	yux@oregonstate.edu	Not Available	Not Available	2024-12-13	View Spectrum
HSQC NMR	[¹H, ¹³C] NMR Spectrum (2D, 700 MHz, CDCl3, experimental)	yux@oregonstate.edu	Not Available	Not Available	2024-12-13	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 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	6.98	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	18	ChemAxon
Refractivity	256.78 m³·mol⁻¹	ChemAxon
Polarizability	104.4 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 [S-Hda]-amatyemide B (NP0350549)

MOL for NP0350549 ([S-Hda]-amatyemide B)

3D MOL for NP0350549 ([S-Hda]-amatyemide B)

3D SDF for NP0350549 ([S-Hda]-amatyemide B)

3D-SDF for NP0350549 ([S-Hda]-amatyemide B)

PDB for NP0350549 ([S-Hda]-amatyemide B)

3D PDB for NP0350549 ([S-Hda]-amatyemide B)

SMILES for NP0350549 ([S-Hda]-amatyemide B)

INCHI for NP0350549 ([S-Hda]-amatyemide B)

Structure for NP0350549 ([S-Hda]-amatyemide B)

3D Structure for NP0350549 ([S-Hda]-amatyemide B)