NP-MRD: Showing NP-Card for 3-bromodeoxyamphimedine (NP0331679)

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Record Information

Version

2.0

Created at

2023-06-09 04:00:19 UTC

Updated at

2025-02-11 15:45:30 UTC

NP-MRD ID

NP0331679

Natural Product DOI

https://doi.org/10.57994/0681

Secondary Accession Numbers

None

Natural Product Identification

Common Name

3-bromodeoxyamphimedine

Description

3-Bromodeoxyamphimedine belongs to the class of organic compounds known as pyrido[2,3,4-kl]acridines. These are organic heterocyclic compounds with a structure based on the pyrido[2,3,4-kl]acridine skeleton. 3-bromodeoxyamphimedine was first documented in 2023 (PMID: 37163243). Based on a literature review very few articles have been published on 3-bromodeoxyamphimedine.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652306092306002D          

 24 28  0  0  0  0            999 V2000
   -3.7637    0.1007    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9535    0.2566    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
   -2.4135   -0.3671    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6033   -0.2111    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3333    0.5684    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5231    0.7243    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0169    0.1007    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.8271    0.2566    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3672   -0.3671    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1773   -0.2111    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4473    0.5684    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2575    0.7243    0.0000 Br  0  0  0  0  0  0  0  0  0  0  0  0
    1.9073    1.1921    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0971    1.0361    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5570    1.6598    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2531    1.5039    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7932    2.1275    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5231    2.9071    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.2870    3.0630    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8271    2.4393    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8734    1.1921    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6033    1.9716    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434    2.5952    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6835    1.0361    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  9 10  1  0  0  0  0
 10 11  2  0  0  0  0
 11 12  1  0  0  0  0
 11 13  1  0  0  0  0
 13 14  2  0  0  0  0
  8 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  2  0  0  0  0
  6 16  1  0  0  0  0
 16 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
 15 20  1  0  0  0  0
  5 21  1  0  0  0  0
 21 22  1  0  0  0  0
 17 22  1  0  0  0  0
 22 23  2  0  0  0  0
 21 24  2  0  0  0  0
  2 24  1  0  0  0  0
M  CHG  1   2   1
M  END
> <DATABASE_ID>
NP0331679

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[N+]1=CC=C2C(=C1)C(=O)C1=NC=CC3=C1C2=NC1=CC=C(Br)C=C31

> <INCHI_IDENTIFIER>
InChI=1S/C19H11BrN3O/c1-23-7-5-12-14(9-23)19(24)18-16-11(4-6-21-18)13-8-10(20)2-3-15(13)22-17(12)16/h2-9H,1H3/q+1

> <INCHI_KEY>
IIUFZSFOIPFHCN-UHFFFAOYSA-N

> <FORMULA>
C19H11BrN3O

> <MOLECULAR_WEIGHT>
377.22

> <EXACT_MASS>
376.008001

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
35

> <JCHEM_AVERAGE_POLARIZABILITY>
36.01069221752185

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
1

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
16-bromo-5-methyl-8-oxo-5,10,20-triazapentacyclo[11.7.1.0^{2,7}.0^{9,21}.0^{14,19}]henicosa-1(20),2,4,6,9,11,13(21),14,16,18-decaen-5-ium

> <JCHEM_LOGP>
-0.5845501258050789

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_ACIDIC>
18.303952406567642

> <JCHEM_PKA_STRONGEST_BASIC>
1.6584544219655775

> <JCHEM_POLAR_SURFACE_AREA>
46.730000000000004

> <JCHEM_REFRACTIVITY>
94.80359999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
16-bromo-5-methyl-8-oxo-5,10,20-triazapentacyclo[11.7.1.0^{2,7}.0^{9,21}.0^{14,19}]henicosa-1(20),2,4,6,9,11,13(21),14,16,18-decaen-5-ium

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 09-JUN-23   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   09-JUN-23         0                                  
HETATM    1  C   UNK     0      -7.026   0.188   0.000  0.00  0.00           C+0
HETATM    2  N   UNK     0      -5.513   0.479   0.000  0.00  0.00           N+1
HETATM    3  C   UNK     0      -4.505  -0.685   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -2.993  -0.394   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -2.489   1.061   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -0.977   1.352   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0       0.032   0.188   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0       1.544   0.479   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       2.552  -0.685   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       4.064  -0.394   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       4.568   1.061   0.000  0.00  0.00           C+0
HETATM   12 Br   UNK     0       6.081   1.352   0.000  0.00  0.00          Br+0
HETATM   13  C   UNK     0       3.560   2.225   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       2.048   1.934   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       1.040   3.098   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      -0.472   2.807   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      -1.481   3.971   0.000  0.00  0.00           C+0
HETATM   18  N   UNK     0      -0.977   5.427   0.000  0.00  0.00           N+0
HETATM   19  C   UNK     0       0.536   5.718   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       1.544   4.553   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      -3.497   2.225   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      -2.993   3.680   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0      -4.001   4.844   0.000  0.00  0.00           O+0
HETATM   24  C   UNK     0      -5.009   1.934   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3   24                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6   21                                                  
CONECT    6    5    7   16                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9   14                                                  
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11   14                                                       
CONECT   14   13    8   15                                                  
CONECT   15   14   16   20                                                  
CONECT   16   15    6   17                                                  
CONECT   17   16   18   22                                                  
CONECT   18   17   19                                                       
CONECT   19   18   20                                                       
CONECT   20   19   15                                                       
CONECT   21    5   22   24                                                  
CONECT   22   21   17   23                                                  
CONECT   23   22                                                            
CONECT   24   21    2                                                       
MASTER        0    0    0    0    0    0    0    0   24    0   56    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₉H₁₁BrN₃O

Average Mass

377.2200 Da

Monoisotopic Mass

376.00800 Da

IUPAC Name

16-bromo-5-methyl-8-oxo-5,10,20-triazapentacyclo[11.7.1.0^{2,7}.0^{9,21}.0^{14,19}]henicosa-1(20),2,4,6,9,11,13(21),14,16,18-decaen-5-ium

Traditional Name

16-bromo-5-methyl-8-oxo-5,10,20-triazapentacyclo[11.7.1.0^{2,7}.0^{9,21}.0^{14,19}]henicosa-1(20),2,4,6,9,11,13(21),14,16,18-decaen-5-ium

CAS Registry Number

Not Available

SMILES

C[N+]1=CC=C2C(=C1)C(=O)C1=NC=CC3=C1C2=NC1=CC=C(Br)C=C31

InChI Identifier

InChI=1S/C19H11BrN3O/c1-23-7-5-12-14(9-23)19(24)18-16-11(4-6-21-18)13-8-10(20)2-3-15(13)22-17(12)16/h2-9H,1H3/q+1

InChI Key

IIUFZSFOIPFHCN-UHFFFAOYSA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹H NMR Spectrum (1D, 600 MHz, CD3OD, experimental)	lucero.martinezfructuoso@nih.gov	Not Available	Not Available	2024-05-11	View Spectrum
HSQC NMR	[¹H, ¹³C] NMR Spectrum (2D, 600 MHz, CD3OD, experimental)	lucero.martinezfructuoso@nih.gov	Not Available	Not Available	2024-05-11	View Spectrum
HMBC NMR	[¹H, ¹³C] NMR Spectrum (2D, 600 MHz, CD3OD, experimental)	lucero.martinezfructuoso@nih.gov	Not Available	Not Available	2024-05-11	View Spectrum
COSY NMR	[¹H, ¹H] NMR Spectrum (2D, 600 MHz, CD3OD, experimental)	lucero.martinezfructuoso@nih.gov	Not Available	Not Available	2024-05-11	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, CD3OD, experimental)	lucero.martinezfructuoso@nih.gov	Not Available	Not Available	2024-05-11	View Spectrum

Predicted Spectra

Not Available

Chemical Shift Submissions

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹H NMR Spectrum (1D, 600, CD₃OD, simulated)	lucero.martinezfructuoso@nih.gov	National Cancer Institute	Lucero Martinez Fructuoso	2024-05-11	View Spectrum

Species

Species of Origin

Species Name	Source	Reference
Moorena sp.		Not Available

Chemical Taxonomy

Description

This compound belongs to the class of organic compounds known as pyrido[2,3,4-kl]acridines. These are organic heterocyclic compounds with a structure based on the pyrido[2,3,4-kl]acridine skeleton.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Quinolines and derivatives

Sub Class

Benzoquinolines

Direct Parent

Pyrido[2,3,4-kl]acridines

Alternative Parents

Substituents

Pyrido[2,3,4-kl]acridine
1,8-phenanthroline
4-phenylpyridine
Haloquinoline
Diazanaphthalene
Naphthyridine
Aryl ketone
Quinonimine
M-quinonimine
2-halopyridine
Alpha-branched alpha,beta-unsaturated-ketone
Benzenoid
Pyridine
Heteroaromatic compound
Vinylogous amide
Alpha,beta-unsaturated ketone
Secondary ketimine
Enone
Acryloyl-group
Ketone
Ketimine
Azacycle
Bromoalkene
Haloalkene
Vinyl halide
Vinyl bromide
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Organonitrogen compound
Organobromide
Organohalogen compound
Imine
Organic cation
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	-0.58	ChemAxon
pKa (Strongest Acidic)	18.3	ChemAxon
pKa (Strongest Basic)	1.66	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	46.73 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	94.8 m³·mol⁻¹	ChemAxon
Polarizability	36.01 Å³	ChemAxon
Number of Rings	5	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

Not Available

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

DOI: 10.1021/acsinfecdis.3c00067

Showing NP-Card for 3-bromodeoxyamphimedine (NP0331679)

MOL for NP0331679 (3-bromodeoxyamphimedine)

3D MOL for NP0331679 (3-bromodeoxyamphimedine)

3D SDF for NP0331679 (3-bromodeoxyamphimedine)

3D-SDF for NP0331679 (3-bromodeoxyamphimedine)

PDB for NP0331679 (3-bromodeoxyamphimedine)

3D PDB for NP0331679 (3-bromodeoxyamphimedine)

SMILES for NP0331679 (3-bromodeoxyamphimedine)

INCHI for NP0331679 (3-bromodeoxyamphimedine)

Structure for NP0331679 (3-bromodeoxyamphimedine)

3D Structure for NP0331679 (3-bromodeoxyamphimedine)