NP-MRD: Showing NP-Card for n-[(10z)-5,8-dihydroxy-3-isopropyl-7-(2-methylpropyl)-2-oxa-6,9-diazabicyclo[10.2.2]hexadeca-1(14),5,8,10,12,15-hexaen-4-yl]-2-(dimethylamino)propanimidic acid (NP0325837)

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Record Information

Version

2.0

Created at

2022-09-12 06:54:05 UTC

Updated at

2022-09-12 06:54:06 UTC

NP-MRD ID

NP0325837

Secondary Accession Numbers

None

Natural Product Identification

Common Name

n-[(10z)-5,8-dihydroxy-3-isopropyl-7-(2-methylpropyl)-2-oxa-6,9-diazabicyclo[10.2.2]hexadeca-1(14),5,8,10,12,15-hexaen-4-yl]-2-(dimethylamino)propanimidic acid

Description

Nummularine K belongs to the class of organic compounds known as oligopeptides. These are organic compounds containing a sequence of between three and ten alpha-amino acids joined by peptide bonds. n-[(10z)-5,8-dihydroxy-3-isopropyl-7-(2-methylpropyl)-2-oxa-6,9-diazabicyclo[10.2.2]hexadeca-1(14),5,8,10,12,15-hexaen-4-yl]-2-(dimethylamino)propanimidic acid is found in Ziziphus xylopyrus. It was first documented in 2015 (PMID: 26361730). Based on a literature review very few articles have been published on Nummularine K.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309122208542D          

 33 34  0  0  0  0            999 V2000
    7.2308    0.2519    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.5536    1.0111    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.3726    1.1112    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.0575    1.6703    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2386    1.5703    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.1493    0.7420    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.7139    0.0328    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.3047   -0.5431    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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  5 32  1  0  0  0  0
 32 33  1  0  0  0  0
M  END

     RDKit          3D

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M  END


  Mrv1652309122208542D          

 33 34  0  0  0  0            999 V2000
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M  END
> <DATABASE_ID>
NP0325837

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(C)CC1N=C(O)C(N=C(O)C(C)N(C)C)C(OC2=CC=C(C=C2)\C=C/N=C1O)C(C)C

> <INCHI_IDENTIFIER>
InChI=1S/C25H38N4O4/c1-15(2)14-20-24(31)26-13-12-18-8-10-19(11-9-18)33-22(16(3)4)21(25(32)27-20)28-23(30)17(5)29(6)7/h8-13,15-17,20-22H,14H2,1-7H3,(H,26,31)(H,27,32)(H,28,30)/b13-12-

> <INCHI_KEY>
SHRVBKXXKGVCPY-SEYXRHQNSA-N

> <FORMULA>
C25H38N4O4

> <MOLECULAR_WEIGHT>
458.603

> <EXACT_MASS>
458.28930572

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_ATOM_COUNT>
71

> <JCHEM_AVERAGE_POLARIZABILITY>
49.22441860844814

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
N-[(10Z)-5,8-dihydroxy-7-(2-methylpropyl)-3-(propan-2-yl)-2-oxa-6,9-diazabicyclo[10.2.2]hexadeca-1(14),5,8,10,12,15-hexaen-4-yl]-2-(dimethylamino)propanimidic acid

> <JCHEM_LOGP>
-2.8917215073479525

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
-4.229127410254308

> <JCHEM_PKA_STRONGEST_ACIDIC>
-9.364801149998542

> <JCHEM_PKA_STRONGEST_BASIC>
14.964448808608493

> <JCHEM_POLAR_SURFACE_AREA>
110.24000000000001

> <JCHEM_REFRACTIVITY>
129.73970000000003

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
N-[(10Z)-5,8-dihydroxy-3-isopropyl-7-(2-methylpropyl)-2-oxa-6,9-diazabicyclo[10.2.2]hexadeca-1(14),5,8,10,12,15-hexaen-4-yl]-2-(dimethylamino)propanimidic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 12-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   12-SEP-22         0                                  
HETATM    1  C   UNK     0      13.498   0.470   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      14.100   1.887   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      15.629   2.074   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      13.174   3.118   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      11.645   2.931   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0      11.479   1.385   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0      10.666   0.061   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      11.769  -1.014   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       9.361  -0.786   0.000  0.00  0.00           C+0
HETATM   10  N   UNK     0       9.894  -2.231   0.000  0.00  0.00           N+0
HETATM   11  C   UNK     0      11.412  -2.492   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0      12.397  -1.308   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0      11.945  -3.937   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      10.961  -5.121   0.000  0.00  0.00           C+0
HETATM   15  N   UNK     0      13.463  -4.197   0.000  0.00  0.00           N+0
HETATM   16  C   UNK     0      14.448  -3.013   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      13.996  -5.642   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       7.805  -0.991   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       7.685  -2.527   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       6.295  -3.191   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       8.955  -3.398   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0       6.288  -0.544   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0       5.291   0.733   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       4.088   1.752   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       4.364   3.274   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       5.782   3.941   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       6.924   2.914   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       6.701   1.394   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       6.843   5.163   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       8.303   5.825   0.000  0.00  0.00           C+0
HETATM   31  N   UNK     0       9.888   5.511   0.000  0.00  0.00           N+0
HETATM   32  C   UNK     0      11.097   4.432   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0      12.371   5.296   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5                                                       
CONECT    5    4    6   32                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10   18                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13   16   17                                                  
CONECT   16   15                                                            
CONECT   17   15                                                            
CONECT   18    9   19   22                                                  
CONECT   19   18   20   21                                                  
CONECT   20   19                                                            
CONECT   21   19                                                            
CONECT   22   18   23                                                       
CONECT   23   22   24   28                                                  
CONECT   24   23   25                                                       
CONECT   25   24   26                                                       
CONECT   26   25   27   29                                                  
CONECT   27   26   28                                                       
CONECT   28   27   23                                                       
CONECT   29   26   30                                                       
CONECT   30   29   31                                                       
CONECT   31   30   32                                                       
CONECT   32   31    5   33                                                  
CONECT   33   32                                                            
MASTER        0    0    0    0    0    0    0    0   33    0   68    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₅H₃₈N₄O₄

Average Mass

458.6030 Da

Monoisotopic Mass

458.28931 Da

IUPAC Name

N-[(10Z)-5,8-dihydroxy-7-(2-methylpropyl)-3-(propan-2-yl)-2-oxa-6,9-diazabicyclo[10.2.2]hexadeca-1(14),5,8,10,12,15-hexaen-4-yl]-2-(dimethylamino)propanimidic acid

Traditional Name

N-[(10Z)-5,8-dihydroxy-3-isopropyl-7-(2-methylpropyl)-2-oxa-6,9-diazabicyclo[10.2.2]hexadeca-1(14),5,8,10,12,15-hexaen-4-yl]-2-(dimethylamino)propanimidic acid

CAS Registry Number

Not Available

SMILES

CC(C)CC1N=C(O)C(N=C(O)C(C)N(C)C)C(OC2=CC=C(C=C2)\C=C/N=C1O)C(C)C

InChI Identifier

InChI=1S/C25H38N4O4/c1-15(2)14-20-24(31)26-13-12-18-8-10-19(11-9-18)33-22(16(3)4)21(25(32)27-20)28-23(30)17(5)29(6)7/h8-13,15-17,20-22H,14H2,1-7H3,(H,26,31)(H,27,32)(H,28,30)/b13-12-

InChI Key

SHRVBKXXKGVCPY-SEYXRHQNSA-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, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, 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
Ziziphus xylopyrus	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as oligopeptides. These are organic compounds containing a sequence of between three and ten alpha-amino acids joined by peptide bonds.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

Oligopeptides

Alternative Parents

Substituents

Alpha-oligopeptide
Cyclic alpha peptide
Macrolactam
N-acyl-alpha amino acid or derivatives
Alpha-amino acid amide
Alanine or derivatives
Alpha-amino acid or derivatives
Alkyl aryl ether
Benzenoid
Amino acid or derivatives
Carboxamide group
Lactam
Tertiary aliphatic amine
Tertiary amine
Secondary carboxylic acid amide
Oxacycle
Ether
Azacycle
Organoheterocyclic compound
Organic oxygen compound
Organic nitrogen compound
Hydrocarbon derivative
Carbonyl group
Organic oxide
Organopnictogen compound
Amine
Organooxygen compound
Organonitrogen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

Not Available

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	-2.9	ChemAxon
pKa (Strongest Acidic)	-9.4	ChemAxon
pKa (Strongest Basic)	14.96	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	8	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	110.24 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	129.74 m³·mol⁻¹	ChemAxon
Polarizability	49.22 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	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

101421018

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Kang KB, Ming G, Kim GJ, Ha TK, Choi H, Oh WK, Sung SH: Jubanines F-J, cyclopeptide alkaloids from the roots of Ziziphus jujuba. Phytochemistry. 2015 Nov;119:90-5. doi: 10.1016/j.phytochem.2015.09.001. Epub 2015 Sep 8. [PubMed:26361730 ]
LOTUS database [Link]

Showing NP-Card for n-[(10z)-5,8-dihydroxy-3-isopropyl-7-(2-methylpropyl)-2-oxa-6,9-diazabicyclo[10.2.2]hexadeca-1(14),5,8,10,12,15-hexaen-4-yl]-2-(dimethylamino)propanimidic acid (NP0325837)

MOL for NP0325837 (n-[(10z)-5,8-dihydroxy-3-isopropyl-7-(2-methylpropyl)-2-oxa-6,9-diazabicyclo[10.2.2]hexadeca-1(14),5,8,10,12,15-hexaen-4-yl]-2-(dimethylamino)propanimidic acid)

3D MOL for NP0325837 (n-[(10z)-5,8-dihydroxy-3-isopropyl-7-(2-methylpropyl)-2-oxa-6,9-diazabicyclo[10.2.2]hexadeca-1(14),5,8,10,12,15-hexaen-4-yl]-2-(dimethylamino)propanimidic acid)

3D SDF for NP0325837 (n-[(10z)-5,8-dihydroxy-3-isopropyl-7-(2-methylpropyl)-2-oxa-6,9-diazabicyclo[10.2.2]hexadeca-1(14),5,8,10,12,15-hexaen-4-yl]-2-(dimethylamino)propanimidic acid)

3D-SDF for NP0325837 (n-[(10z)-5,8-dihydroxy-3-isopropyl-7-(2-methylpropyl)-2-oxa-6,9-diazabicyclo[10.2.2]hexadeca-1(14),5,8,10,12,15-hexaen-4-yl]-2-(dimethylamino)propanimidic acid)

PDB for NP0325837 (n-[(10z)-5,8-dihydroxy-3-isopropyl-7-(2-methylpropyl)-2-oxa-6,9-diazabicyclo[10.2.2]hexadeca-1(14),5,8,10,12,15-hexaen-4-yl]-2-(dimethylamino)propanimidic acid)

3D PDB for NP0325837 (n-[(10z)-5,8-dihydroxy-3-isopropyl-7-(2-methylpropyl)-2-oxa-6,9-diazabicyclo[10.2.2]hexadeca-1(14),5,8,10,12,15-hexaen-4-yl]-2-(dimethylamino)propanimidic acid)

SMILES for NP0325837 (n-[(10z)-5,8-dihydroxy-3-isopropyl-7-(2-methylpropyl)-2-oxa-6,9-diazabicyclo[10.2.2]hexadeca-1(14),5,8,10,12,15-hexaen-4-yl]-2-(dimethylamino)propanimidic acid)

INCHI for NP0325837 (n-[(10z)-5,8-dihydroxy-3-isopropyl-7-(2-methylpropyl)-2-oxa-6,9-diazabicyclo[10.2.2]hexadeca-1(14),5,8,10,12,15-hexaen-4-yl]-2-(dimethylamino)propanimidic acid)

Structure for NP0325837 (n-[(10z)-5,8-dihydroxy-3-isopropyl-7-(2-methylpropyl)-2-oxa-6,9-diazabicyclo[10.2.2]hexadeca-1(14),5,8,10,12,15-hexaen-4-yl]-2-(dimethylamino)propanimidic acid)

3D Structure for NP0325837 (n-[(10z)-5,8-dihydroxy-3-isopropyl-7-(2-methylpropyl)-2-oxa-6,9-diazabicyclo[10.2.2]hexadeca-1(14),5,8,10,12,15-hexaen-4-yl]-2-(dimethylamino)propanimidic acid)