NP-MRD: Showing NP-Card for (-)-Arborescidine B (NP0068669)

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Record Information

Version

2.0

Created at

2022-04-28 13:56:05 UTC

Updated at

2022-04-28 13:56:05 UTC

NP-MRD ID

NP0068669

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(-)-Arborescidine B

Description

(3AR)-3-Methyl-9-bromo-1,2,3,3a,4,5-hexahydro-3,7a-diaza-7aH-cyclohepta[jk]fluorene belongs to the class of organic compounds known as beta carbolines. Beta carbolines are compounds containing a 9H-pyrido[3,4-b]indole moiety. (-)-Arborescidine B is found in Pseudodistoma arborescens. Based on a literature review very few articles have been published on (3aR)-3-Methyl-9-bromo-1,2,3,3a,4,5-hexahydro-3,7a-diaza-7aH-cyclohepta[jk]fluorene.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 36 39  0  0  0  0  0  0  0  0999 V2000
   -3.4401   -1.5151   -0.0501 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0635   -1.3383   -0.5422 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3382   -2.4799   -0.1134 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1316   -2.4103   -0.1864 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7016   -1.0578   -0.2435 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1084    0.0376   -0.1894 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6734    1.1089   -0.2610 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.9794    0.7215   -0.3609 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1730    1.4069   -0.4616 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3760    0.7456   -0.5507 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9754    1.7848   -0.6868 Br  0  0  0  0  0  0  0  0  0  0  0  0
    4.4047   -0.6325   -0.5404 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2243   -1.3228   -0.4407 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0067   -0.6566   -0.3504 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3591    2.4823   -0.2491 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8395    3.0279   -0.1742 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1328    2.3419   -0.0853 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1713    1.0578   -0.8875 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5663   -0.0810   -0.0730 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.9051   -2.2716   -0.7033 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3290   -1.9673    0.9787 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9776   -0.5783    0.0432 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7019   -2.7515    0.9206 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6777   -3.3501   -0.7475 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5596   -3.0161   -1.0239 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5499   -2.8942    0.7451 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1470    2.5034   -0.4695 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3839   -1.1203   -0.6134 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2333   -2.4024   -0.4315 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1875    3.1926   -0.3077 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8448    4.1230   -0.1807 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9091    3.0480   -0.4777 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4004    2.0987    0.9734 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2129    0.8729   -1.1686 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6079    1.1919   -1.8481 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8398    0.1003    0.9973 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  2  0
  6 19  1  0
 19 18  1  0
 18 17  1  0
 17 16  1  0
 16 15  2  0
 15  7  1  0
  7  8  1  0
  8  9  2  0
  9 10  1  0
 10 11  1  0
 10 12  2  0
 12 13  1  0
 13 14  2  0
 19  2  1  0
 14  8  1  0
 14  5  1  0
  7  6  1  0
  1 20  1  0
  1 21  1  0
  1 22  1  0
  3 23  1  0
  3 24  1  0
  4 25  1  0
  4 26  1  0
 19 36  1  1
 18 34  1  0
 18 35  1  0
 17 32  1  0
 17 33  1  0
 16 31  1  0
 15 30  1  0
  9 27  1  0
 12 28  1  0
 13 29  1  0
M  END


  Mrv1652304282215562D          

 19 22  0  0  1  0            999 V2000
    5.1043    1.0920    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8360    1.8721    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0262    2.0299    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4847    1.4074    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7530    0.6273    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5628    0.4695    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0939    0.1310    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4183    0.6045    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6599    1.3934    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.1937    2.0740    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3709    2.1340    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8110    1.5280    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9357    0.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6510    0.3015    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.5983   -0.5657    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.2739   -1.0392    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0217   -0.6908    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8552   -0.9241    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3775    2.4945    0.0000 Br  0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  1  6  1  0  0  0  0
  5  7  1  0  0  0  0
  7  8  2  0  0  0  0
  8  9  1  0  0  0  0
  4  9  1  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
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14  8  1  6  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
  7 17  1  0  0  0  0
 15 18  1  0  0  0  0
  2 19  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0068669

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CN1CCC2=C3[C@H]1CCC=CN3C1=CC(Br)=CC=C21

> <INCHI_IDENTIFIER>
InChI=1S/C16H17BrN2/c1-18-9-7-13-12-6-5-11(17)10-15(12)19-8-3-2-4-14(18)16(13)19/h3,5-6,8,10,14H,2,4,7,9H2,1H3/t14-/m1/s1

> <INCHI_KEY>
IGXMRBGOOHQACP-CQSZACIVSA-N

> <FORMULA>
C16H17BrN2

> <MOLECULAR_WEIGHT>
317.23

> <EXACT_MASS>
316.057512

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
36

> <JCHEM_AVERAGE_POLARIZABILITY>
31.553756543764223

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(5R)-13-bromo-4-methyl-4,10-diazatetracyclo[8.6.1.0^{5,17}.0^{11,16}]heptadeca-1(17),8,11,13,15-pentaene

> <ALOGPS_LOGP>
4.16

> <JCHEM_LOGP>
3.887835143666667

> <ALOGPS_LOGS>
-3.50

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_BASIC>
7.3262893397783255

> <JCHEM_POLAR_SURFACE_AREA>
8.17

> <JCHEM_REFRACTIVITY>
83.29910000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.00e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(5R)-13-bromo-4-methyl-4,10-diazatetracyclo[8.6.1.0^{5,17}.0^{11,16}]heptadeca-1(17),8,11,13,15-pentaene

> <JCHEM_VEBER_RULE>
1

$$$$

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  C   UNK     0       9.528   2.038   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       9.027   3.495   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       7.516   3.789   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       6.505   2.627   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       7.006   1.171   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       8.517   0.876   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       5.775   0.245   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       4.514   1.128   0.000  0.00  0.00           C+0
HETATM    9  N   UNK     0       4.965   2.601   0.000  0.00  0.00           N+0
HETATM   10  C   UNK     0       4.095   3.872   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       2.559   3.983   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       1.514   2.852   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       1.747   1.330   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       3.082   0.563   0.000  0.00  0.00           C+0
HETATM   15  N   UNK     0       2.983  -1.056   0.000  0.00  0.00           N+0
HETATM   16  C   UNK     0       4.245  -1.940   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       5.641  -1.289   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       1.596  -1.725   0.000  0.00  0.00           C+0
HETATM   19 Br   UNK     0      10.038   4.656   0.000  0.00  0.00          Br+0
CONECT    1    2    6                                                       
CONECT    2    1    3   19                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5    9                                                  
CONECT    5    4    6    7                                                  
CONECT    6    5    1                                                       
CONECT    7    5    8   17                                                  
CONECT    8    7    9   14                                                  
CONECT    9    8    4   10                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13    8   15                                                  
CONECT   15   14   16   18                                                  
CONECT   16   15   17                                                       
CONECT   17   16    7                                                       
CONECT   18   15                                                            
CONECT   19    2                                                            
MASTER        0    0    0    0    0    0    0    0   19    0   44    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₆H₁₇BrN₂

Average Mass

317.2300 Da

Monoisotopic Mass

316.05751 Da

IUPAC Name

(5R)-13-bromo-4-methyl-4,10-diazatetracyclo[8.6.1.0^{5,17}.0^{11,16}]heptadeca-1(17),8,11,13,15-pentaene

Traditional Name

(5R)-13-bromo-4-methyl-4,10-diazatetracyclo[8.6.1.0^{5,17}.0^{11,16}]heptadeca-1(17),8,11,13,15-pentaene

CAS Registry Number

Not Available

SMILES

CN1CCC2=C3[C@H]1CCC=CN3C1=CC(Br)=CC=C21

InChI Identifier

InChI=1S/C16H17BrN2/c1-18-9-7-13-12-6-5-11(17)10-15(12)19-8-3-2-4-14(18)16(13)19/h3,5-6,8,10,14H,2,4,7,9H2,1H3/t14-/m1/s1

InChI Key

IGXMRBGOOHQACP-CQSZACIVSA-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
Pseudodistoma arborescens	-	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as beta carbolines. Beta carbolines are compounds containing a 9H-pyrido[3,4-b]indole moiety.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Indoles and derivatives

Sub Class

Pyridoindoles

Direct Parent

Beta carbolines

Alternative Parents

Substituents

Beta-carboline
Pyrroloazepine
3-alkylindole
Indole
Azepine
Aralkylamine
Aryl bromide
Aryl halide
Benzenoid
Pyrrole
Heteroaromatic compound
Tertiary amine
Tertiary aliphatic amine
Azacycle
Organonitrogen compound
Organobromide
Organohalogen compound
Hydrocarbon derivative
Organic nitrogen compound
Amine
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	4.16	ALOGPS
logP	3.89	ChemAxon
logS	-3.5	ALOGPS
pKa (Strongest Basic)	7.33	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	1	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	8.17 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	83.3 m³·mol⁻¹	ChemAxon
Polarizability	31.55 Å³	ChemAxon
Number of Rings	4	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	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

9601975

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

11427099

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for (-)-Arborescidine B (NP0068669)

MOL for NP0068669 ((-)-Arborescidine B)

3D MOL for NP0068669 ((-)-Arborescidine B)

3D SDF for NP0068669 ((-)-Arborescidine B)

3D-SDF for NP0068669 ((-)-Arborescidine B)

PDB for NP0068669 ((-)-Arborescidine B)

3D PDB for NP0068669 ((-)-Arborescidine B)

SMILES for NP0068669 ((-)-Arborescidine B)

INCHI for NP0068669 ((-)-Arborescidine B)

Structure for NP0068669 ((-)-Arborescidine B)

3D Structure for NP0068669 ((-)-Arborescidine B)