NP-MRD: Showing NP-Card for Isocaulamidine D (NP0332189)

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Record Information

Version

2.0

Created at

2023-12-01 20:02:37 UTC

Updated at

2024-09-03 04:18:20 UTC

NP-MRD ID

NP0332189

Natural Product DOI

https://doi.org/10.57994/1358

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Isocaulamidine D

Description

Isocaulamidine D belongs to the class of organic compounds known as naphthyridines. Naphthyridines are compounds containing a naphthyridine moiety, a naphthalene in which a carbon atom has been replaced by a nitrogen in each of the two rings. The naphthyridine skeleton can also be described as an assembly two fused pyridine rings, which do not share their nitrogen atom. Isocaulamidine D was first documented in 2023 (PMID: 37792337). Based on a literature review very few articles have been published on Isocaulamidine D (PMID: 37368408).

Structure

MOL SDF PDB SMILES InChI


  Mrv2104 12012320022D          

 29 34  0  0  1  0            999 V2000
    5.9415    3.0218    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8926    2.1983    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    6.6150    1.7483    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.4243    1.9087    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    7.8269    1.1886    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.3586    0.6547    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.5106   -0.2049    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.3151   -0.3875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.8755    0.2180    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.6314    1.0060    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.5109    0.8740    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    7.1683    0.3754    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    7.9287    0.6954    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    7.0652   -0.4431    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.3048   -0.7631    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.6474   -0.2646    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8870   -0.5846    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.7839   -1.4031    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2297   -0.0860    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3328    0.7325    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6754    1.2310    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9150    0.9110    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8119    0.0925    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0515   -0.2275    0.0000 Br  0  0  0  0  0  0  0  0  0  0  0  0
    3.4693   -0.4060    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1853    1.1240    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7505    0.5540    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.9303    0.8829    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0804    1.8174    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  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
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
  5 10  1  0  0  0  0
 11  6  1  6  0  0  0
 11  3  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  6  0  0  0
 12 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  2  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 17 19  1  0  0  0  0
 19 20  2  0  0  0  0
 20 21  1  0  0  0  0
 21 22  2  0  0  0  0
 22 23  1  0  0  0  0
 23 24  1  0  0  0  0
 23 25  2  0  0  0  0
 19 25  1  0  0  0  0
 20 26  1  0  0  0  0
 27 16  1  1  0  0  0
 11 27  1  0  0  0  0
 27 26  1  0  0  0  0
 27 28  1  0  0  0  0
 28 29  1  0  0  0  0
  2 29  1  0  0  0  0
M  END


  Mrv2104 12012320022D          

 29 34  0  0  1  0            999 V2000
    5.9415    3.0218    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8926    2.1983    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    6.6150    1.7483    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.4243    1.9087    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    7.8269    1.1886    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.3586    0.6547    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.5106   -0.2049    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.3151   -0.3875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.8755    0.2180    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.6314    1.0060    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.5109    0.8740    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    7.1683    0.3754    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    7.9287    0.6954    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    7.0652   -0.4431    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.3048   -0.7631    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.6474   -0.2646    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8870   -0.5846    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.7839   -1.4031    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2297   -0.0860    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3328    0.7325    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6754    1.2310    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9150    0.9110    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8119    0.0925    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0515   -0.2275    0.0000 Br  0  0  0  0  0  0  0  0  0  0  0  0
    3.4693   -0.4060    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1853    1.1240    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7505    0.5540    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.9303    0.8829    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0804    1.8174    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  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
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
  5 10  1  0  0  0  0
 11  6  1  6  0  0  0
 11  3  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  6  0  0  0
 12 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  2  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 17 19  1  0  0  0  0
 19 20  2  0  0  0  0
 20 21  1  0  0  0  0
 21 22  2  0  0  0  0
 22 23  1  0  0  0  0
 23 24  1  0  0  0  0
 23 25  2  0  0  0  0
 19 25  1  0  0  0  0
 20 26  1  0  0  0  0
 27 16  1  1  0  0  0
 11 27  1  0  0  0  0
 27 26  1  0  0  0  0
 27 28  1  0  0  0  0
 28 29  1  0  0  0  0
  2 29  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0332189

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CN1CC[C@@]23CC4=C(C=C(Br)C=C4)N(C)C2=NC[C@@H](Cl)[C@]32C1=NC1=C2C=CC=C1

> <INCHI_IDENTIFIER>
InChI=1S/C23H22BrClN4/c1-28-10-9-22-12-14-7-8-15(24)11-18(14)29(2)20(22)26-13-19(25)23(22)16-5-3-4-6-17(16)27-21(23)28/h3-8,11,19H,9-10,12-13H2,1-2H3/t19-,22-,23-/m1/s1

> <INCHI_KEY>
FGGMONMSXOUBCE-UEVCKROQSA-N

> <FORMULA>
C23H22BrClN4

> <MOLECULAR_WEIGHT>
469.81

> <EXACT_MASS>
468.071637

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
51

> <JCHEM_AVERAGE_POLARIZABILITY>
46.00318992808696

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(1R,13S,14S)-6-bromo-13-chloro-9,23-dimethyl-9,11,21,23-tetraazahexacyclo[12.11.0.0^{1,10}.0^{3,8}.0^{14,22}.0^{15,20}]pentacosa-3(8),4,6,10,15(20),16,18,21-octaene

> <JCHEM_LOGP>
4.515626037666667

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
6

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
5.565486833842673

> <JCHEM_POLAR_SURFACE_AREA>
31.200000000000003

> <JCHEM_REFRACTIVITY>
123.0062

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(1R,13S,14S)-6-bromo-13-chloro-9,23-dimethyl-9,11,21,23-tetraazahexacyclo[12.11.0.0^{1,10}.0^{3,8}.0^{14,22}.0^{15,20}]pentacosa-3(8),4,6,10,15(20),16,18,21-octaene

> <JCHEM_VEBER_RULE>
1

$$$$

HEADER    PROTEIN                                 01-DEC-23   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   01-DEC-23         0                                  
HETATM    1  C   UNK     0      11.091   5.641   0.000  0.00  0.00           C+0
HETATM    2  N   UNK     0      11.000   4.103   0.000  0.00  0.00           N+0
HETATM    3  C   UNK     0      12.348   3.264   0.000  0.00  0.00           C+0
HETATM    4  N   UNK     0      13.859   3.563   0.000  0.00  0.00           N+0
HETATM    5  C   UNK     0      14.610   2.219   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      13.736   1.222   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      14.020  -0.382   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      15.522  -0.723   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      16.568   0.407   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      16.112   1.878   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      12.154   1.631   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      13.381   0.701   0.000  0.00  0.00           C+0
HETATM   13 Cl   UNK     0      14.800   1.298   0.000  0.00  0.00          Cl+0
HETATM   14  C   UNK     0      13.188  -0.827   0.000  0.00  0.00           C+0
HETATM   15  N   UNK     0      11.769  -1.424   0.000  0.00  0.00           N+0
HETATM   16  C   UNK     0      10.542  -0.494   0.000  0.00  0.00           C+0
HETATM   17  N   UNK     0       9.122  -1.091   0.000  0.00  0.00           N+0
HETATM   18  C   UNK     0       8.930  -2.619   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       7.895  -0.161   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       8.088   1.367   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       6.861   2.298   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       5.441   1.701   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       5.249   0.173   0.000  0.00  0.00           C+0
HETATM   24 Br   UNK     0       3.830  -0.425   0.000  0.00  0.00          Br+0
HETATM   25  C   UNK     0       6.476  -0.758   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       9.679   2.098   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      10.734   1.034   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       9.203   1.648   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       9.483   3.393   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3   29                                                  
CONECT    3    2    4   11                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6   10                                                  
CONECT    6    5    7   11                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9    5                                                       
CONECT   11    6    3   12   27                                             
CONECT   12   11   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15   17   27                                                  
CONECT   17   16   18   19                                                  
CONECT   18   17                                                            
CONECT   19   17   20   25                                                  
CONECT   20   19   21   26                                                  
CONECT   21   20   22                                                       
CONECT   22   21   23                                                       
CONECT   23   22   24   25                                                  
CONECT   24   23                                                            
CONECT   25   23   19                                                       
CONECT   26   20   27                                                       
CONECT   27   16   11   26   28                                             
CONECT   28   27   29                                                       
CONECT   29   28    2                                                       
MASTER        0    0    0    0    0    0    0    0   29    0   68    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₃H₂₂BrClN₄

Average Mass

469.8100 Da

Monoisotopic Mass

468.07164 Da

IUPAC Name

(1R,13S,14S)-6-bromo-13-chloro-9,23-dimethyl-9,11,21,23-tetraazahexacyclo[12.11.0.0^{1,10}.0^{3,8}.0^{14,22}.0^{15,20}]pentacosa-3(8),4,6,10,15(20),16,18,21-octaene

Traditional Name

(1R,13S,14S)-6-bromo-13-chloro-9,23-dimethyl-9,11,21,23-tetraazahexacyclo[12.11.0.0^{1,10}.0^{3,8}.0^{14,22}.0^{15,20}]pentacosa-3(8),4,6,10,15(20),16,18,21-octaene

CAS Registry Number

Not Available

SMILES

CN1CC[C@@]23CC4=C(C=C(Br)C=C4)N(C)C2=NC[C@@H](Cl)[C@]32C1=NC1=C2C=CC=C1

InChI Identifier

InChI=1S/C23H22BrClN4/c1-28-10-9-22-12-14-7-8-15(24)11-18(14)29(2)20(22)26-13-19(25)23(22)16-5-3-4-6-17(16)27-21(23)28/h3-8,11,19H,9-10,12-13H2,1-2H3/t19-,22-,23-/m1/s1

InChI Key

FGGMONMSXOUBCE-UEVCKROQSA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
NOESY NMR	[¹H, ¹H] NMR Spectrum (2D, 600 MHz, CD3OD, experimental)	dongdong.wang@nih.gov	NCI-Frederick	Dong Wang	2024-05-09	View Spectrum
HMBC NMR	[¹H, ¹³C] NMR Spectrum (2D, 600 MHz, CD3OD, experimental)	dongdong.wang@nih.gov	NCI-Frederick	Dong Wang	2024-05-09	View Spectrum
HSQC NMR	[¹H, ¹³C] NMR Spectrum (2D, 600 MHz, CD3OD, experimental)	dongdong.wang@nih.gov	NCI-Frederick	Dong Wang	2024-05-09	View Spectrum
COSY NMR	[¹H, ¹H] NMR Spectrum (2D, 600 MHz, CD3OD, experimental)	dongdong.wang@nih.gov	NCI-Frederick	Dong Wang	2024-05-09	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, CD3OD, experimental)	dongdong.wang@nih.gov	NCI-Frederick	Dong Wang	2024-05-09	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, CD3OD, experimental)	dongdong.wang@nih.gov	NCI-Frederick	Dong Wang	2024-05-09	View Spectrum

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
sp.		Not Available

Chemical Taxonomy

Description

This compound belongs to the class of organic compounds known as naphthyridines. These are compounds containing a naphthyridine moiety, a naphthalene in which a carbon atom has been replaced by a nitrogen in each of the two rings. The naphthyridine skeleton can also be described as an assembly two fused pyridine rings, which do not share their nitrogen atom.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Diazanaphthalenes

Sub Class

Naphthyridines

Direct Parent

Naphthyridines

Alternative Parents

Substituents

3-alkylindole
Naphthyridine
Tetrahydroquinoline
Azaspirodecane
Indole or derivatives
Tetrahydropyridine
Imidolactam
Benzenoid
Piperidine
Azacycle
Bromoalkene
Haloalkene
Organic 1,3-dipolar compound
Propargyl-type 1,3-dipolar organic compound
Carboximidamide
Vinyl halide
Vinyl bromide
Amidine
Organic nitrogen compound
Organopnictogen compound
Hydrocarbon derivative
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	4.52	ChemAxon
pKa (Strongest Basic)	5.57	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	31.2 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	123.01 m³·mol⁻¹	ChemAxon
Polarizability	46 Å³	ChemAxon
Number of Rings	6	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

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

Yu H, Zhang J, Ma D, Li X, Xu T: Enantioselective Total Syntheses of (-)-Caulamidine D and (-)-Isocaulamidine D and Their Absolute Configuration Reassignment. J Am Chem Soc. 2023 Oct 18;145(41):22335-22340. doi: 10.1021/jacs.3c08714. Epub 2023 Oct 4. [PubMed:37792337 ]
Tian X, Wang D, Jiang W, Bokesch HR, Wilson BAP, O'Keefe BR, Gustafson KR: Rare Caulamidine Hexacyclic Alkaloids from the Marine Ascidian Polyandrocarpa sp. J Nat Prod. 2023 Jul 28;86(7):1855-1861. doi: 10.1021/acs.jnatprod.3c00393. Epub 2023 Jun 27. [PubMed:37368408 ]

Showing NP-Card for Isocaulamidine D (NP0332189)

MOL for NP0332189 (Isocaulamidine D)

3D MOL for NP0332189 (Isocaulamidine D)

3D SDF for NP0332189 (Isocaulamidine D)

3D-SDF for NP0332189 (Isocaulamidine D)

PDB for NP0332189 (Isocaulamidine D)

3D PDB for NP0332189 (Isocaulamidine D)

SMILES for NP0332189 (Isocaulamidine D)

INCHI for NP0332189 (Isocaulamidine D)

Structure for NP0332189 (Isocaulamidine D)

3D Structure for NP0332189 (Isocaulamidine D)