NP-MRD: Showing NP-Card for (+)-Nagelamide O (NP0081372)

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Record Information

Version

2.0

Created at

2022-04-29 02:20:38 UTC

Updated at

2022-04-29 02:20:38 UTC

NP-MRD ID

NP0081372

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(+)-Nagelamide O

Description

3-Bromo-N-{[(1S,2S,6S,10S,11S,12S,13S,14S)-14-chloro-13-{[(4,5-dibromo-1H-pyrrol-2-yl)formamido]methyl}-2,10-dihydroxy-4,8-diimino-3,5,7,9-tetraazatetracyclo[9.3.0.0¹,⁵.0⁶,¹⁰]Tetradecan-12-yl]methyl}-1H-pyrrole-2-carboximidic acid belongs to the class of organic compounds known as iridoids and derivatives. These are monoterpenes containing a skeleton structurally characterized by the presence of a cylopentane fused to a pyran ( forming a 4,7-dimethylcyclopenta[c]pyran), or a derivative where the pentane moiety is open. (+)-Nagelamide O is found in Agelas sp. Based on a literature review very few articles have been published on 3-bromo-N-{[(1S,2S,6S,10S,11S,12S,13S,14S)-14-chloro-13-{[(4,5-dibromo-1H-pyrrol-2-yl)formamido]methyl}-2,10-dihydroxy-4,8-diimino-3,5,7,9-tetraazatetracyclo[9.3.0.0¹,⁵.0⁶,¹⁰]Tetradecan-12-yl]methyl}-1H-pyrrole-2-carboximidic acid.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304292204202D          

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M  END

     RDKit          3D

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M  END


  Mrv1652304292204202D          

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  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
  9 11  1  0  0  0  0
 11 12  2  0  0  0  0
 12 13  1  0  0  0  0
 13 14  2  0  0  0  0
 14 15  1  0  0  0  0
 11 15  1  0  0  0  0
 14 16  1  0  0  0  0
 13 17  1  0  0  0  0
  3 18  1  1  0  0  0
 18 19  1  0  0  0  0
 19 20  1  0  0  0  0
 20 21  2  0  0  0  0
 20 22  1  0  0  0  0
 22 23  1  0  0  0  0
 23 24  1  0  0  0  0
 24 25  2  0  0  0  0
 25 26  1  0  0  0  0
 22 26  2  0  0  0  0
 26 27  1  0  0  0  0
  2 28  1  0  0  0  0
 28 29  1  0  0  0  0
 29 30  1  1  0  0  0
  1 30  1  1  0  0  0
 30 31  1  0  0  0  0
 31 32  2  0  0  0  0
 32 33  1  0  0  0  0
  1 33  1  0  0  0  0
 33 34  1  1  0  0  0
 31 35  1  0  0  0  0
 29 36  1  0  0  0  0
 36 37  1  0  0  0  0
 37 38  2  0  0  0  0
 28 38  1  0  0  0  0
 37 39  1  0  0  0  0
 28 40  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0081372

> <DATABASE_NAME>
NP-MRD

> <SMILES>
NC1=N[C@@]2(O)[C@@H](N1)N1C(N)=N[C@@H](O)[C@@]11[C@@H](Cl)[C@H](CNC(=O)C3=CC(Br)=C(Br)N3)[C@@H](CNC(=O)C3=C(Br)C=CN3)[C@H]21

> <INCHI_IDENTIFIER>
InChI=1S/C22H24Br3ClN10O4/c23-8-1-2-29-11(8)16(38)31-4-6-7(5-30-15(37)10-3-9(24)14(25)32-10)13(26)21-12(6)22(40)17(33-19(27)35-22)36(21)20(28)34-18(21)39/h1-3,6-7,12-13,17-18,29,32,39-40H,4-5H2,(H2,28,34)(H,30,37)(H,31,38)(H3,27,33,35)/t6-,7-,12+,13+,17+,18+,21-,22+/m1/s1

> <INCHI_KEY>
QJPOEKBYXGAXIH-JPQGAVBOSA-N

> <FORMULA>
C22H24Br3ClN10O4

> <MOLECULAR_WEIGHT>
767.66

> <EXACT_MASS>
763.922066

> <JCHEM_ACCEPTOR_COUNT>
10

> <JCHEM_ATOM_COUNT>
64

> <JCHEM_AVERAGE_POLARIZABILITY>
62.90829449061678

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
9

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
4,5-dibromo-N-{[(1S,2S,6S,10S,11S,12S,13S,14S)-4,8-diamino-12-{[(3-bromo-1H-pyrrol-2-yl)formamido]methyl}-14-chloro-2,10-dihydroxy-3,5,7,9-tetraazatetracyclo[9.3.0.0^{1,5}.0^{6,10}]tetradeca-3,8-dien-13-yl]methyl}-1H-pyrrole-2-carboxamide

> <ALOGPS_LOGP>
1.52

> <JCHEM_LOGP>
0.2965972950000004

> <ALOGPS_LOGS>
-3.71

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
6

> <JCHEM_PHYSIOLOGICAL_CHARGE>
2

> <JCHEM_PKA>
11.70238699112078

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.000978334893057

> <JCHEM_PKA_STRONGEST_BASIC>
7.481219468743221

> <JCHEM_POLAR_SURFACE_AREA>
222.26999999999998

> <JCHEM_REFRACTIVITY>
153.24020000000004

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.50e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
4,5-dibromo-N-{[(1S,2S,6S,10S,11S,12S,13S,14S)-4,8-diamino-12-{[(3-bromo-1H-pyrrol-2-yl)formamido]methyl}-14-chloro-2,10-dihydroxy-3,5,7,9-tetraazatetracyclo[9.3.0.0^{1,5}.0^{6,10}]tetradeca-3,8-dien-13-yl]methyl}-1H-pyrrole-2-carboxamide

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 29-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   29-APR-22         0                                  
HETATM    1  C   UNK     0       1.175  -2.306   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.651  -0.841   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.405   0.064   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -0.841  -0.841   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -0.365  -2.306   0.000  0.00  0.00           C+0
HETATM    6 Cl   UNK     0      -1.270  -3.552   0.000  0.00  0.00          Cl+0
HETATM    7  C   UNK     0      -2.306  -0.365   0.000  0.00  0.00           C+0
HETATM    8  N   UNK     0      -3.450  -1.396   0.000  0.00  0.00           N+0
HETATM    9  C   UNK     0      -4.915  -0.920   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      -5.235   0.587   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0      -6.059  -1.950   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -5.898  -3.482   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -7.305  -4.108   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -8.336  -2.964   0.000  0.00  0.00           C+0
HETATM   15  N   UNK     0      -7.566  -1.630   0.000  0.00  0.00           N+0
HETATM   16 Br   UNK     0      -9.867  -3.125   0.000  0.00  0.00          Br+0
HETATM   17 Br   UNK     0      -7.625  -5.615   0.000  0.00  0.00          Br+0
HETATM   18  C   UNK     0       0.405   1.604   0.000  0.00  0.00           C+0
HETATM   19  N   UNK     0      -0.929   2.374   0.000  0.00  0.00           N+0
HETATM   20  C   UNK     0      -0.929   3.914   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0       0.405   4.684   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0      -2.263   4.684   0.000  0.00  0.00           C+0
HETATM   23  N   UNK     0      -3.669   4.058   0.000  0.00  0.00           N+0
HETATM   24  C   UNK     0      -4.700   5.202   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      -3.930   6.536   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      -2.424   6.216   0.000  0.00  0.00           C+0
HETATM   27 Br   UNK     0      -1.279   7.246   0.000  0.00  0.00          Br+0
HETATM   28  C   UNK     0       3.191  -0.841   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       3.667  -2.306   0.000  0.00  0.00           C+0
HETATM   30  N   UNK     0       2.421  -3.211   0.000  0.00  0.00           N+0
HETATM   31  C   UNK     0       1.945  -4.676   0.000  0.00  0.00           C+0
HETATM   32  N   UNK     0       0.405  -4.676   0.000  0.00  0.00           N+0
HETATM   33  C   UNK     0      -0.071  -3.211   0.000  0.00  0.00           C+0
HETATM   34  O   UNK     0      -1.317  -4.116   0.000  0.00  0.00           O+0
HETATM   35  N   UNK     0       2.850  -5.921   0.000  0.00  0.00           N+0
HETATM   36  N   UNK     0       5.207  -2.306   0.000  0.00  0.00           N+0
HETATM   37  C   UNK     0       5.682  -0.841   0.000  0.00  0.00           C+0
HETATM   38  N   UNK     0       4.437   0.064   0.000  0.00  0.00           N+0
HETATM   39  N   UNK     0       7.147  -0.365   0.000  0.00  0.00           N+0
HETATM   40  O   UNK     0       2.715   0.624   0.000  0.00  0.00           O+0
CONECT    1    2    5   30   33                                             
CONECT    2    1    3   28                                                  
CONECT    3    2    4   18                                                  
CONECT    4    3    5    7                                                  
CONECT    5    4    1    6                                                  
CONECT    6    5                                                            
CONECT    7    4    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9   12   15                                                  
CONECT   12   11   13                                                       
CONECT   13   12   14   17                                                  
CONECT   14   13   15   16                                                  
CONECT   15   14   11                                                       
CONECT   16   14                                                            
CONECT   17   13                                                            
CONECT   18    3   19                                                       
CONECT   19   18   20                                                       
CONECT   20   19   21   22                                                  
CONECT   21   20                                                            
CONECT   22   20   23   26                                                  
CONECT   23   22   24                                                       
CONECT   24   23   25                                                       
CONECT   25   24   26                                                       
CONECT   26   25   22   27                                                  
CONECT   27   26                                                            
CONECT   28    2   29   38   40                                             
CONECT   29   28   30   36                                                  
CONECT   30   29    1   31                                                  
CONECT   31   30   32   35                                                  
CONECT   32   31   33                                                       
CONECT   33   32    1   34                                                  
CONECT   34   33                                                            
CONECT   35   31                                                            
CONECT   36   29   37                                                       
CONECT   37   36   38   39                                                  
CONECT   38   37   28                                                       
CONECT   39   37                                                            
CONECT   40   28                                                            
MASTER        0    0    0    0    0    0    0    0   40    0   90    0
END

View in JSmol

Synonyms

Value	Source
3-Bromo-N-{[(1S,2S,6S,10S,11S,12S,13S,14S)-14-chloro-13-{[(4,5-dibromo-1H-pyrrol-2-yl)formamido]methyl}-2,10-dihydroxy-4,8-diimino-3,5,7,9-tetraazatetracyclo[9.3.0.0,.0,]tetradecan-12-yl]methyl}-1H-pyrrole-2-carboximidate	Generator

Chemical Formula

C₂₂H₂₄Br₃ClN₁₀O₄

Average Mass

767.6600 Da

Monoisotopic Mass

763.92207 Da

IUPAC Name

4,5-dibromo-N-{[(1S,2S,6S,10S,11S,12S,13S,14S)-4,8-diamino-12-{[(3-bromo-1H-pyrrol-2-yl)formamido]methyl}-14-chloro-2,10-dihydroxy-3,5,7,9-tetraazatetracyclo[9.3.0.0^{1,5}.0^{6,10}]tetradeca-3,8-dien-13-yl]methyl}-1H-pyrrole-2-carboxamide

Traditional Name

CAS Registry Number

Not Available

SMILES

NC1=N[C@@]2(O)[C@@H](N1)N1C(N)=N[C@@H](O)[C@@]11[C@@H](Cl)[C@H](CNC(=O)C3=CC(Br)=C(Br)N3)[C@@H](CNC(=O)C3=C(Br)C=CN3)[C@H]21

InChI Identifier

InChI=1S/C22H24Br3ClN10O4/c23-8-1-2-29-11(8)16(38)31-4-6-7(5-30-15(37)10-3-9(24)14(25)32-10)13(26)21-12(6)22(40)17(33-19(27)35-22)36(21)20(28)34-18(21)39/h1-3,6-7,12-13,17-18,29,32,39-40H,4-5H2,(H2,28,34)(H,30,37)(H,31,38)(H3,27,33,35)/t6-,7-,12+,13+,17+,18+,21-,22+/m1/s1

InChI Key

QJPOEKBYXGAXIH-JPQGAVBOSA-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, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, 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
Agelas sp.	Animalia	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as iridoids and derivatives. These are monoterpenes containing a skeleton structurally characterized by the presence of a cylopentane fused to a pyran ( forming a 4,7-dimethylcyclopenta[c]pyran), or a derivative where the pentane moiety is open.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Monoterpenoids

Direct Parent

Iridoids and derivatives

Alternative Parents

Substituents

11-noriridane monoterpenoid
Aromatic monoterpenoid
2-heteroaryl carboxamide
Pyrrole-2-carboxylic acid or derivatives
Pyrrole-2-carboxamide
Substituted pyrrole
Aryl halide
Aryl bromide
Heteroaromatic compound
Vinylogous halide
Pyrrolidine
Pyrrole
2-imidazoline
Secondary carboxylic acid amide
Guanidine
Carboxamide group
Azacycle
Organoheterocyclic compound
Organic 1,3-dipolar compound
Propargyl-type 1,3-dipolar organic compound
Carboximidamide
Carboxylic acid derivative
Alkanolamine
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Organonitrogen compound
Organochloride
Organobromide
Organohalogen compound
Alkyl halide
Alkyl chloride
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	1.52	ALOGPS
logP	0.3	ChemAxon
logS	-3.7	ALOGPS
pKa (Strongest Acidic)	11	ChemAxon
pKa (Strongest Basic)	7.48	ChemAxon
Physiological Charge	2	ChemAxon
Hydrogen Acceptor Count	10	ChemAxon
Hydrogen Donor Count	9	ChemAxon
Polar Surface Area	222.27 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	153.24 m³·mol⁻¹	ChemAxon
Polarizability	62.91 Å³	ChemAxon
Number of Rings	6	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

163030110

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for (+)-Nagelamide O (NP0081372)

MOL for NP0081372 ((+)-Nagelamide O)

3D MOL for NP0081372 ((+)-Nagelamide O)

3D SDF for NP0081372 ((+)-Nagelamide O)

3D-SDF for NP0081372 ((+)-Nagelamide O)

PDB for NP0081372 ((+)-Nagelamide O)

3D PDB for NP0081372 ((+)-Nagelamide O)

SMILES for NP0081372 ((+)-Nagelamide O)

INCHI for NP0081372 ((+)-Nagelamide O)

Structure for NP0081372 ((+)-Nagelamide O)

3D Structure for NP0081372 ((+)-Nagelamide O)