NP-MRD: Showing NP-Card for Polyneurine B (NP0332057)

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Record Information

Version

1.0

Created at

2023-10-31 20:04:11 UTC

Updated at

2024-05-11 13:24:20 UTC

NP-MRD ID

NP0332057

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Polyneurine B

Description

Not Available

Structure

MOL SDF PDB SMILES InChI


  Mrv2104 10312320042D          

 29 32  0  0  1  0            999 V2000
    4.8592    3.3415    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0423    3.4568    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.5506    4.1066    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.3675    3.9913    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2420    4.8717    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2254    3.5721    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.4194    3.7482    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7170    2.9223    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.0256    2.1572    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8425    2.0419    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.1511    1.2768    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9680    1.1615    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.3509    2.6917    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2587    2.2364    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6236    1.4964    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1653    0.8105    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5610    1.7961    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8921    2.9146    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3717    3.5548    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5477    4.3608    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2876    4.7257    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0343    4.3747    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.6020    3.2577    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1337    3.6308    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8248    3.1802    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7801    2.3564    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0443    1.9832    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6468    2.4339    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4441    2.2218    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  6  0  0  0
  2  3  1  0  0  0  0
  3  4  1  1  0  0  0
  3  5  1  0  0  0  0
  2  6  1  0  0  0  0
  6  7  1  6  0  0  0
  6  8  1  0  0  0  0
  8  9  1  0  0  0  0
 10  9  1  0  0  0  0
 10 11  1  1  0  0  0
 11 12  1  0  0  0  0
 10 13  1  0  0  0  0
  2 13  1  0  0  0  0
  8 14  1  6  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 14 17  2  0  0  0  0
  8 18  1  0  0  0  0
 18 19  2  0  0  0  0
 19 20  1  0  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
  6 22  1  0  0  0  0
 19 23  1  0  0  0  0
 23 24  2  0  0  0  0
 24 25  1  0  0  0  0
 25 26  2  0  0  0  0
 26 27  1  0  0  0  0
 27 28  2  0  0  0  0
 23 28  1  0  0  0  0
 28 29  1  0  0  0  0
 18 29  1  0  0  0  0
M  END


  Mrv2104 10312320042D          

 29 32  0  0  1  0            999 V2000
    4.8592    3.3415    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0423    3.4568    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.5506    4.1066    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.3675    3.9913    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2420    4.8717    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2254    3.5721    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.4194    3.7482    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7170    2.9223    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.0256    2.1572    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8425    2.0419    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.1511    1.2768    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9680    1.1615    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.3509    2.6917    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2587    2.2364    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6236    1.4964    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1653    0.8105    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5610    1.7961    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8921    2.9146    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3717    3.5548    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5477    4.3608    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2876    4.7257    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0343    4.3747    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.6020    3.2577    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1337    3.6308    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8248    3.1802    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7801    2.3564    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0443    1.9832    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6468    2.4339    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4441    2.2218    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  6  0  0  0
  2  3  1  0  0  0  0
  3  4  1  1  0  0  0
  3  5  1  0  0  0  0
  2  6  1  0  0  0  0
  6  7  1  6  0  0  0
  6  8  1  0  0  0  0
  8  9  1  0  0  0  0
 10  9  1  0  0  0  0
 10 11  1  1  0  0  0
 11 12  1  0  0  0  0
 10 13  1  0  0  0  0
  2 13  1  0  0  0  0
  8 14  1  6  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 14 17  2  0  0  0  0
  8 18  1  0  0  0  0
 18 19  2  0  0  0  0
 19 20  1  0  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
  6 22  1  0  0  0  0
 19 23  1  0  0  0  0
 23 24  2  0  0  0  0
 24 25  1  0  0  0  0
 25 26  2  0  0  0  0
 26 27  1  0  0  0  0
 27 28  2  0  0  0  0
 23 28  1  0  0  0  0
 28 29  1  0  0  0  0
 18 29  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0332057

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H][C@@]1(C[C@@H](CO)C[C@@]2(C(=O)OC)C3=C(CCN[C@@]12[H])C1=CC=CC=C1N3)[C@@H](C)O

> <INCHI_IDENTIFIER>
InChI=1S/C21H28N2O4/c1-12(25)16-9-13(11-24)10-21(20(26)27-2)18(16)22-8-7-15-14-5-3-4-6-17(14)23-19(15)21/h3-6,12-13,16,18,22-25H,7-11H2,1-2H3/t12-,13-,16-,18+,21+/m1/s1

> <INCHI_KEY>
PZPOFNRIYGFPDQ-KQPNIRENSA-N

> <FORMULA>
C21H28N2O4

> <MOLECULAR_WEIGHT>
372.465

> <EXACT_MASS>
372.20490739

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
55

> <JCHEM_AVERAGE_POLARIZABILITY>
41.41436960959358

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
methyl (2S,4R,6S,7S)-6-[(1R)-1-hydroxyethyl]-4-(hydroxymethyl)-8,18-diazatetracyclo[9.7.0.0^{2,7}.0^{12,17}]octadeca-1(11),12,14,16-tetraene-2-carboxylate

> <JCHEM_LOGP>
1.1941281579999998

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
15.605122054729135

> <JCHEM_PKA_STRONGEST_ACIDIC>
15.005773456353907

> <JCHEM_PKA_STRONGEST_BASIC>
9.183440940068838

> <JCHEM_POLAR_SURFACE_AREA>
94.57999999999998

> <JCHEM_REFRACTIVITY>
102.5528

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
methyl (2S,4R,6S,7S)-6-[(1R)-1-hydroxyethyl]-4-(hydroxymethyl)-8,18-diazatetracyclo[9.7.0.0^{2,7}.0^{12,17}]octadeca-1(11),12,14,16-tetraene-2-carboxylate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 31-OCT-23   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   31-OCT-23         0                                  
HETATM    1  H   UNK     0       9.070   6.237   0.000  0.00  0.00           H+0
HETATM    2  C   UNK     0       7.546   6.453   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       8.494   7.666   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0      10.019   7.450   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       7.918   9.094   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       6.021   6.668   0.000  0.00  0.00           C+0
HETATM    7  H   UNK     0       4.516   6.997   0.000  0.00  0.00           H+0
HETATM    8  C   UNK     0       5.072   5.455   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       5.648   4.027   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       7.173   3.812   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       7.749   2.383   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       9.274   2.168   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0       8.122   5.025   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       4.216   4.175   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0       4.897   2.793   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0       4.042   1.513   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0       2.914   3.353   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0       3.532   5.441   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       2.560   6.636   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       2.889   8.140   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       4.270   8.821   0.000  0.00  0.00           C+0
HETATM   22  N   UNK     0       5.664   8.166   0.000  0.00  0.00           N+0
HETATM   23  C   UNK     0       1.124   6.081   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      -0.250   6.778   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      -1.540   5.936   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      -1.456   4.399   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      -0.083   3.702   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       1.207   4.543   0.000  0.00  0.00           C+0
HETATM   29  N   UNK     0       2.696   4.147   0.000  0.00  0.00           N+0
CONECT    1    2                                                            
CONECT    2    1    3    6   13                                             
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3                                                            
CONECT    6    2    7    8   22                                             
CONECT    7    6                                                            
CONECT    8    6    9   14   18                                             
CONECT    9    8   10                                                       
CONECT   10    9   11   13                                                  
CONECT   11   10   12                                                       
CONECT   12   11                                                            
CONECT   13   10    2                                                       
CONECT   14    8   15   17                                                  
CONECT   15   14   16                                                       
CONECT   16   15                                                            
CONECT   17   14                                                            
CONECT   18    8   19   29                                                  
CONECT   19   18   20   23                                                  
CONECT   20   19   21                                                       
CONECT   21   20   22                                                       
CONECT   22   21    6                                                       
CONECT   23   19   24   28                                                  
CONECT   24   23   25                                                       
CONECT   25   24   26                                                       
CONECT   26   25   27                                                       
CONECT   27   26   28                                                       
CONECT   28   27   23   29                                                  
CONECT   29   28   18                                                       
MASTER        0    0    0    0    0    0    0    0   29    0   64    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₁H₂₈N₂O₄

Average Mass

372.4650 Da

Monoisotopic Mass

372.20491 Da

IUPAC Name

methyl (2S,4R,6S,7S)-6-[(1R)-1-hydroxyethyl]-4-(hydroxymethyl)-8,18-diazatetracyclo[9.7.0.0^{2,7}.0^{12,17}]octadeca-1(11),12,14,16-tetraene-2-carboxylate

Traditional Name

methyl (2S,4R,6S,7S)-6-[(1R)-1-hydroxyethyl]-4-(hydroxymethyl)-8,18-diazatetracyclo[9.7.0.0^{2,7}.0^{12,17}]octadeca-1(11),12,14,16-tetraene-2-carboxylate

CAS Registry Number

Not Available

SMILES

[H][C@@]1(C[C@@H](CO)C[C@@]2(C(=O)OC)C3=C(CCN[C@@]12[H])C1=CC=CC=C1N3)[C@@H](C)O

InChI Identifier

InChI=1S/C21H28N2O4/c1-12(25)16-9-13(11-24)10-21(20(26)27-2)18(16)22-8-7-15-14-5-3-4-6-17(14)23-19(15)21/h3-6,12-13,16,18,22-25H,7-11H2,1-2H3/t12-,13-,16-,18+,21+/m1/s1

InChI Key

PZPOFNRIYGFPDQ-KQPNIRENSA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
1D_DEPT NMR	¹³C NMR Spectrum (1D, 101 MHz, CDCl3, experimental)	yylow@um.edu.my	Department of Chemistry, Faculty of Science, Universiti Malaya	Yun-Yee Low	2024-05-11	View Spectrum
HMBC NMR	[¹H, ¹³C] NMR Spectrum (2D, 400 MHz, CDCl3, experimental)	yylow@um.edu.my	Department of Chemistry, Faculty of Science, Universiti Malaya	Yun-Yee Low	2023-10-31	View Spectrum
COSY NMR	[¹H, ¹H] NMR Spectrum (2D, 400 MHz, CDCl3, experimental)	yylow@um.edu.my	Department of Chemistry, Faculty of Science, Universiti Malaya	Yun-Yee Low	2023-10-31	View Spectrum
HSQC NMR	[¹H, ¹³C] NMR Spectrum (2D, 400 MHz, CDCl3, experimental)	yylow@um.edu.my	Department of Chemistry, Faculty of Science, Universiti Malaya	Yun-Yee Low	2023-10-31	View Spectrum
1D NMR	[¹³C, ] NMR Spectrum (2D, 101 MHz, CDCl3, experimental)	yylow@um.edu.my	Department of Chemistry, Faculty of Science, Universiti Malaya	Yun-Yee Low	2023-10-31	View Spectrum
1D NMR	[¹H, ] NMR Spectrum (2D, 400 MHz, CDCl3, experimental)	yylow@um.edu.my	Department of Chemistry, Faculty of Science, Universiti Malaya	Yun-Yee Low	2023-10-31	View Spectrum
NOESY NMR	[¹H, ¹H] NMR Spectrum (2D, 400 MHz, CDCl3, experimental)	yylow@um.edu.my	Department of Chemistry, Faculty of Science, Universiti Malaya	Yun-Yee Low	2023-10-31	View Spectrum

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
polyneura		Not Available

Chemical Taxonomy

Classification

Not classified

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	1.19	ChemAxon
pKa (Strongest Acidic)	15.01	ChemAxon
pKa (Strongest Basic)	9.18	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	94.58 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	102.55 m³·mol⁻¹	ChemAxon
Polarizability	41.41 Å³	ChemAxon
Number of Rings	4	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

Not Available

References

General References

Tang SY, Tan CH, Sim KS, Yong KT, Lim KH, Low YY, Lim SH: Polyneurines A-H, iboga alkaloids from Tabernaemontana polyneura. Phytochemistry. 2023 Apr;208:113587. doi: 10.1016/j.phytochem.2023.113587. Epub 2023 Jan 14. [PubMed:36646163 ]

Showing NP-Card for Polyneurine B (NP0332057)

MOL for NP0332057 (Polyneurine B)

3D MOL for NP0332057 (Polyneurine B)

3D SDF for NP0332057 (Polyneurine B)

3D-SDF for NP0332057 (Polyneurine B)

PDB for NP0332057 (Polyneurine B)

3D PDB for NP0332057 (Polyneurine B)

SMILES for NP0332057 (Polyneurine B)

INCHI for NP0332057 (Polyneurine B)

Structure for NP0332057 (Polyneurine B)

3D Structure for NP0332057 (Polyneurine B)