NP-MRD: Showing NP-Card for Axinellamine B (NP0069602)

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Record Information

Version

2.0

Created at

2022-04-28 14:58:31 UTC

Updated at

2022-04-28 14:58:31 UTC

NP-MRD ID

NP0069602

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Axinellamine B

Description

4,5-Dibromo-N-{[(1R,2R,6S,10S,11R,12R,13R,14R)-14-chloro-12-{[(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-13-yl]methyl}-1H-pyrrole-2-carboxamide 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. Axinellamine B is found in Axinella sp. Based on a literature review very few articles have been published on 4,5-dibromo-N-{[(1R,2R,6S,10S,11R,12R,13R,14R)-14-chloro-12-{[(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-13-yl]methyl}-1H-pyrrole-2-carboxamide.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304282216582D          

 41 46  0  0  1  0            999 V2000
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M  END

     RDKit          3D

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M  END


  Mrv1652304282216582D          

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  5  6  1  0  0  0  0
  7  6  1  6  0  0  0
  8  7  1  1  0  0  0
  4  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
  7 11  1  0  0  0  0
 11 12  1  6  0  0  0
 10 13  1  1  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  2  0  0  0  0
 15 17  1  0  0  0  0
 17 18  2  0  0  0  0
 18 19  1  0  0  0  0
 19 20  2  0  0  0  0
 20 21  1  0  0  0  0
 17 21  1  0  0  0  0
 20 22  1  0  0  0  0
 19 23  1  0  0  0  0
  9 24  1  6  0  0  0
 24 25  1  0  0  0  0
 25 26  1  0  0  0  0
 26 27  2  0  0  0  0
 26 28  1  0  0  0  0
 28 29  1  0  0  0  0
 29 30  1  0  0  0  0
 30 31  2  0  0  0  0
 31 32  1  0  0  0  0
 28 32  2  0  0  0  0
 31 33  1  0  0  0  0
 30 34  1  0  0  0  0
  7 35  1  0  0  0  0
 35 36  1  0  0  0  0
 36 37  2  0  0  0  0
  6 37  1  0  0  0  0
 37 38  1  0  0  0  0
 35 39  1  6  0  0  0
  4 40  1  6  0  0  0
  2 41  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0069602

> <DATABASE_NAME>
NP-MRD

> <SMILES>
NC1=N[C@H]2N3C(N)=N[C@H](O)[C@]33[C@H](Cl)[C@@H](CNC(=O)C4=CC(Br)=C(Br)N4)[C@H](CNC(=O)C4=CC(Br)=C(Br)N4)[C@H]3[C@@]2(O)N1

> <INCHI_IDENTIFIER>
InChI=1S/C22H23Br4ClN10O4/c23-7-1-9(32-13(7)25)15(38)30-3-5-6(4-31-16(39)10-2-8(24)14(26)33-10)12(27)21-11(5)22(41)17(34-19(28)36-22)37(21)20(29)35-18(21)40/h1-2,5-6,11-12,17-18,32-33,40-41H,3-4H2,(H2,29,35)(H,30,38)(H,31,39)(H3,28,34,36)/t5-,6-,11+,12+,17-,18+,21-,22-/m0/s1

> <INCHI_KEY>
NDKURSLTVHZNHX-YNLGVKOTSA-N

> <FORMULA>
C22H23Br4ClN10O4

> <MOLECULAR_WEIGHT>
846.56

> <EXACT_MASS>
841.832579

> <JCHEM_ACCEPTOR_COUNT>
10

> <JCHEM_ATOM_COUNT>
64

> <JCHEM_AVERAGE_POLARIZABILITY>
66.90224012426206

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
9

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
2.20

> <JCHEM_LOGP>
0.7657054133333339

> <ALOGPS_LOGS>
-3.92

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
6

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
11.032699385943474

> <JCHEM_PKA_STRONGEST_ACIDIC>
6.66689563876163

> <JCHEM_PKA_STRONGEST_BASIC>
13.101156361940609

> <JCHEM_POLAR_SURFACE_AREA>
222.26999999999998

> <JCHEM_REFRACTIVITY>
160.64500000000004

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.02e-01 g/l

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

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 28-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   28-APR-22         0                                  
HETATM    1  N   UNK     0       7.576   0.956   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0       8.052   2.421   0.000  0.00  0.00           C+0
HETATM    3  N   UNK     0       6.806   3.326   0.000  0.00  0.00           N+0
HETATM    4  C   UNK     0       5.561   2.421   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       6.036   0.956   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0       4.791   0.051   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0       3.545   0.956   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       4.021   2.421   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       2.775   3.326   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       1.529   2.421   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       2.005   0.956   0.000  0.00  0.00           C+0
HETATM   12 Cl   UNK     0       1.099  -0.290   0.000  0.00  0.00          Cl+0
HETATM   13  C   UNK     0       0.064   2.897   0.000  0.00  0.00           C+0
HETATM   14  N   UNK     0      -1.080   1.866   0.000  0.00  0.00           N+0
HETATM   15  C   UNK     0      -2.545   2.342   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0      -2.865   3.848   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0      -3.689   1.312   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      -3.528  -0.220   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      -4.935  -0.846   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      -5.966   0.298   0.000  0.00  0.00           C+0
HETATM   21  N   UNK     0      -5.196   1.632   0.000  0.00  0.00           N+0
HETATM   22 Br   UNK     0      -7.497   0.137   0.000  0.00  0.00          Br+0
HETATM   23 Br   UNK     0      -5.255  -2.353   0.000  0.00  0.00          Br+0
HETATM   24  C   UNK     0       2.775   4.866   0.000  0.00  0.00           C+0
HETATM   25  N   UNK     0       1.441   5.636   0.000  0.00  0.00           N+0
HETATM   26  C   UNK     0       1.441   7.176   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0       0.107   7.946   0.000  0.00  0.00           O+0
HETATM   28  C   UNK     0       2.775   7.946   0.000  0.00  0.00           C+0
HETATM   29  N   UNK     0       2.936   9.477   0.000  0.00  0.00           N+0
HETATM   30  C   UNK     0       4.442   9.798   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       5.212   8.464   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       4.181   7.320   0.000  0.00  0.00           C+0
HETATM   33 Br   UNK     0       6.744   8.303   0.000  0.00  0.00          Br+0
HETATM   34 Br   UNK     0       5.068  11.204   0.000  0.00  0.00          Br+0
HETATM   35  C   UNK     0       2.299   0.051   0.000  0.00  0.00           C+0
HETATM   36  N   UNK     0       2.775  -1.414   0.000  0.00  0.00           N+0
HETATM   37  C   UNK     0       4.315  -1.414   0.000  0.00  0.00           C+0
HETATM   38  N   UNK     0       5.220  -2.660   0.000  0.00  0.00           N+0
HETATM   39  O   UNK     0       1.053  -0.854   0.000  0.00  0.00           O+0
HETATM   40  O   UNK     0       5.085   3.885   0.000  0.00  0.00           O+0
HETATM   41  N   UNK     0       9.517   2.897   0.000  0.00  0.00           N+0
CONECT    1    2    5                                                       
CONECT    2    1    3   41                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5    8   40                                             
CONECT    5    4    1    6                                                  
CONECT    6    5    7   37                                                  
CONECT    7    6    8   11   35                                             
CONECT    8    7    4    9                                                  
CONECT    9    8   10   24                                                  
CONECT   10    9   11   13                                                  
CONECT   11   10    7   12                                                  
CONECT   12   11                                                            
CONECT   13   10   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   16   17                                                  
CONECT   16   15                                                            
CONECT   17   15   18   21                                                  
CONECT   18   17   19                                                       
CONECT   19   18   20   23                                                  
CONECT   20   19   21   22                                                  
CONECT   21   20   17                                                       
CONECT   22   20                                                            
CONECT   23   19                                                            
CONECT   24    9   25                                                       
CONECT   25   24   26                                                       
CONECT   26   25   27   28                                                  
CONECT   27   26                                                            
CONECT   28   26   29   32                                                  
CONECT   29   28   30                                                       
CONECT   30   29   31   34                                                  
CONECT   31   30   32   33                                                  
CONECT   32   31   28                                                       
CONECT   33   31                                                            
CONECT   34   30                                                            
CONECT   35    7   36   39                                                  
CONECT   36   35   37                                                       
CONECT   37   36    6   38                                                  
CONECT   38   37                                                            
CONECT   39   35                                                            
CONECT   40    4                                                            
CONECT   41    2                                                            
MASTER        0    0    0    0    0    0    0    0   41    0   92    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₂H₂₃Br₄ClN₁₀O₄

Average Mass

846.5600 Da

Monoisotopic Mass

841.83258 Da

IUPAC Name

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

Traditional Name

CAS Registry Number

Not Available

SMILES

NC1=N[C@H]2N3C(N)=N[C@H](O)[C@]33[C@H](Cl)[C@@H](CNC(=O)C4=CC(Br)=C(Br)N4)[C@H](CNC(=O)C4=CC(Br)=C(Br)N4)[C@H]3[C@@]2(O)N1

InChI Identifier

InChI=1S/C22H23Br4ClN10O4/c23-7-1-9(32-13(7)25)15(38)30-3-5-6(4-31-16(39)10-2-8(24)14(26)33-10)12(27)21-11(5)22(41)17(34-19(28)36-22)37(21)20(29)35-18(21)40/h1-2,5-6,11-12,17-18,32-33,40-41H,3-4H2,(H2,29,35)(H,30,38)(H,31,39)(H3,28,34,36)/t5-,6-,11+,12+,17-,18+,21-,22-/m0/s1

InChI Key

NDKURSLTVHZNHX-YNLGVKOTSA-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
Axinella 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
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	2.2	ALOGPS
logP	0.77	ChemAxon
logS	-3.9	ALOGPS
pKa (Strongest Acidic)	6.67	ChemAxon
pKa (Strongest Basic)	13.1	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	10	ChemAxon
Hydrogen Donor Count	9	ChemAxon
Polar Surface Area	222.27 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	160.64 m³·mol⁻¹	ChemAxon
Polarizability	66.9 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

163079102

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Axinellamine B (NP0069602)

MOL for NP0069602 (Axinellamine B)

3D MOL for NP0069602 (Axinellamine B)

3D SDF for NP0069602 (Axinellamine B)

3D-SDF for NP0069602 (Axinellamine B)

PDB for NP0069602 (Axinellamine B)

3D PDB for NP0069602 (Axinellamine B)

SMILES for NP0069602 (Axinellamine B)

INCHI for NP0069602 (Axinellamine B)

Structure for NP0069602 (Axinellamine B)

3D Structure for NP0069602 (Axinellamine B)