Np mrd loader

Showing NP-Card for (±)-Pandamarine (NP0334050)

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Record Information
Version2.0
Created at2024-09-09 21:49:44 UTC
Updated at2024-09-09 21:49:44 UTC
NP-MRD IDNP0334050
Secondary Accession NumbersNone
Natural Product Identification
Common Name(±)-Pandamarine
DescriptionMajor alkaloid from leaves of Pandanus amaryllifolius
Structure
Thumb
MOLSDFPDBSMILESInChI

MOL for NP0334050 ((±)-Pandamarine)


  Mrv2104 05252300222D          

 24 26  0  0  0  0            999 V2000
    4.4440   -2.2624    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6674   -0.4849    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2695   -2.4454    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5070    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6820   -1.7309    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9195    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6820   -3.1599    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6820    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2695   -1.0164    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5070   -0.3020    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9920   -2.4924    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7846   -0.2549    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7766   -2.7474    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5070   -3.1599    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7766   -3.5724    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2695    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9920   -3.8273    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7846    1.0799    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.6820   -0.3020    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.4440   -4.0573    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6674    1.3099    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2695   -3.8743    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  1 13  1  0  0  0  0
  2 14  1  0  0  0  0
  3  5  1  0  0  0  0
  3  7  1  0  0  0  0
  4  6  1  0  0  0  0
  4  8  1  0  0  0  0
  5  9  1  0  0  0  0
  6 10  1  0  0  0  0
  7 24  1  0  0  0  0
  7 15  2  0  0  0  0
  8 18  1  0  0  0  0
  9 21  1  0  0  0  0
 10 21  1  0  0  0  0
 11 13  2  0  0  0  0
 11 15  1  0  0  0  0
 12 14  2  0  0  0  0
 12 18  1  0  0  0  0
 13 16  1  0  0  0  0
 14 17  1  0  0  0  0
 15 19  1  0  0  0  0
 16 19  2  0  0  0  0
 16 22  1  0  0  0  0
 17 20  2  0  0  0  0
 17 23  1  0  0  0  0
 18 20  1  0  0  0  0
 18 21  1  0  0  0  0
M  END
Download

3D MOL for NP0334050 ((±)-Pandamarine)

Download
3D SDF for NP0334050 ((±)-Pandamarine)

  Mrv2104 05252300222D          

 24 26  0  0  0  0            999 V2000
    4.4440   -2.2624    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6674   -0.4849    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2695   -2.4454    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5070    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6820   -1.7309    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9195    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6820   -3.1599    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6820    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2695   -1.0164    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5070   -0.3020    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9920   -2.4924    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7846   -0.2549    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7766   -2.7474    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5070   -3.1599    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7766   -3.5724    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2695    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9920   -3.8273    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7846    1.0799    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.6820   -0.3020    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.4440   -4.0573    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6674    1.3099    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2695   -3.8743    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  1 13  1  0  0  0  0
  2 14  1  0  0  0  0
  3  5  1  0  0  0  0
  3  7  1  0  0  0  0
  4  6  1  0  0  0  0
  4  8  1  0  0  0  0
  5  9  1  0  0  0  0
  6 10  1  0  0  0  0
  7 24  1  0  0  0  0
  7 15  2  0  0  0  0
  8 18  1  0  0  0  0
  9 21  1  0  0  0  0
 10 21  1  0  0  0  0
 11 13  2  0  0  0  0
 11 15  1  0  0  0  0
 12 14  2  0  0  0  0
 12 18  1  0  0  0  0
 13 16  1  0  0  0  0
 14 17  1  0  0  0  0
 15 19  1  0  0  0  0
 16 19  2  0  0  0  0
 16 22  1  0  0  0  0
 17 20  2  0  0  0  0
 17 23  1  0  0  0  0
 18 20  1  0  0  0  0
 18 21  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0334050

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H]\C(CCCN1CCCCC11C=C(C)C(O)=N1)=C1\C=C(C)C(O)=N1

> <INCHI_IDENTIFIER>
InChI=1/C18H25N3O2/c1-13-11-15(19-16(13)22)7-3-5-9-21-10-6-4-8-18(21)12-14(2)17(23)20-18/h7,11-12H,3-6,8-10H2,1-2H3,(H,19,22)(H,20,23)/b15-7+

> <INCHI_KEY>
YMXRBZVJOJYAFJ-VIZOYTHANA-N

> <FORMULA>
C18H25N3O2

> <MOLECULAR_WEIGHT>
315.417

> <EXACT_MASS>
315.194677057

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
48

> <JCHEM_AVERAGE_POLARIZABILITY>
35.997662509583925

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
6-{4-[(2E)-5-hydroxy-4-methylpyrrol-2-ylidene]butyl}-3-methyl-1,6-diazaspiro[4.5]deca-1,3-dien-2-ol

> <JCHEM_LOGP>
1.885769993070629

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
6.199181267104764

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.011656124172186

> <JCHEM_PKA_STRONGEST_BASIC>
6.790604184227136

> <JCHEM_POLAR_SURFACE_AREA>
68.42

> <JCHEM_REFRACTIVITY>
94.5743

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
6-{4-[(2E)-5-hydroxy-4-methylpyrrol-2-ylidene]butyl}-3-methyl-1,6-diazaspiro[4.5]deca-1,3-dien-2-ol

> <JCHEM_VEBER_RULE>
0

$$$$

Download
3D-SDF for NP0334050 ((±)-Pandamarine)
Download
PDB for NP0334050 ((±)-Pandamarine)
HEADER    PROTEIN                                 25-MAY-23   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   25-MAY-23         0                                  
HETATM    1  C   UNK     0       8.296  -4.223   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -1.246  -0.905   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.370  -4.565   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       4.680   2.104   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       3.140  -3.231   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       5.450   0.770   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       3.140  -5.898   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       3.140   2.104   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       2.370  -1.897   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       4.680  -0.564   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       5.585  -4.653   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       1.465  -0.476   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       7.050  -5.128   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       0.000  -0.000   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       4.680  -5.898   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       7.050  -6.668   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      -0.000   1.540   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       2.370   0.770   0.000  0.00  0.00           C+0
HETATM   19  N   UNK     0       5.585  -7.144   0.000  0.00  0.00           N+0
HETATM   20  N   UNK     0       1.465   2.016   0.000  0.00  0.00           N+0
HETATM   21  N   UNK     0       3.140  -0.564   0.000  0.00  0.00           N+0
HETATM   22  O   UNK     0       8.296  -7.574   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0      -1.246   2.445   0.000  0.00  0.00           O+0
HETATM   24  H   UNK     0       2.370  -7.232   0.000  0.00  0.00           H+0
CONECT    1   13                                                            
CONECT    2   14                                                            
CONECT    3    5    7                                                       
CONECT    4    6    8                                                       
CONECT    5    3    9                                                       
CONECT    6    4   10                                                       
CONECT    7    3   24   15                                                  
CONECT    8    4   18                                                       
CONECT    9    5   21                                                       
CONECT   10    6   21                                                       
CONECT   11   13   15                                                       
CONECT   12   14   18                                                       
CONECT   13    1   11   16                                                  
CONECT   14    2   12   17                                                  
CONECT   15    7   11   19                                                  
CONECT   16   13   19   22                                                  
CONECT   17   14   20   23                                                  
CONECT   18    8   12   20   21                                             
CONECT   19   15   16                                                       
CONECT   20   17   18                                                       
CONECT   21    9   10   18                                                  
CONECT   22   16                                                            
CONECT   23   17                                                            
CONECT   24    7                                                            
MASTER        0    0    0    0    0    0    0    0   24    0   52    0
END

Download
3D PDB for NP0334050 ((±)-Pandamarine)
Download
SMILES for NP0334050 ((±)-Pandamarine)
[H]\C(CCCN1CCCCC11C=C(C)C(O)=N1)=C1\C=C(C)C(O)=N1
Download
INCHI for NP0334050 ((±)-Pandamarine)
InChI=1/C18H25N3O2/c1-13-11-15(19-16(13)22)7-3-5-9-21-10-6-4-8-18(21)12-14(2)17(23)20-18/h7,11-12H,3-6,8-10H2,1-2H3,(H,19,22)(H,20,23)/b15-7+
Download
View in JSmol
SynonymsNot Available
Chemical FormulaC18H25N3O2
Average Mass315.4170 Da
Monoisotopic Mass315.19468 Da
IUPAC Name6-{4-[(2E)-5-hydroxy-4-methylpyrrol-2-ylidene]butyl}-3-methyl-1,6-diazaspiro[4.5]deca-1,3-dien-2-ol
Traditional Name6-{4-[(2E)-5-hydroxy-4-methylpyrrol-2-ylidene]butyl}-3-methyl-1,6-diazaspiro[4.5]deca-1,3-dien-2-ol
CAS Registry NumberNot Available
SMILES
[H]\C(CCCN1CCCCC11C=C(C)C(O)=N1)=C1\C=C(C)C(O)=N1
InChI Identifier
InChI=1/C18H25N3O2/c1-13-11-15(19-16(13)22)7-3-5-9-21-10-6-4-8-18(21)12-14(2)17(23)20-18/h7,11-12H,3-6,8-10H2,1-2H3,(H,19,22)(H,20,23)/b15-7+
InChI KeyYMXRBZVJOJYAFJ-VIZOYTHANA-N
Experimental Spectra
Not Available
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of OriginNot Available
Chemical Taxonomy
ClassificationNot classified
Physical Properties
StateNot Available
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP1.89ChemAxon
pKa (Strongest Acidic)4.01ChemAxon
pKa (Strongest Basic)6.79ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area68.42 ŲChemAxon
Rotatable Bond Count4ChemAxon
Refractivity94.57 m³·mol⁻¹ChemAxon
Polarizability36 ųChemAxon
Number of Rings3ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDNot Available
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem CompoundNot Available
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References