NP-MRD: Showing NP-Card for Dendrine (NP0064397)

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Record Information

Version

2.0

Created at

2022-04-28 08:38:14 UTC

Updated at

2022-04-28 08:38:14 UTC

NP-MRD ID

NP0064397

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Dendrine

Description

Methyl 2-[(1S,3S,4S,7S,8S,11R,12R,13S)-2,12-dimethyl-9-oxo-13-(propan-2-yl)-10-oxa-2-azatetracyclo[5.4.1.1⁸,¹¹.0⁴,¹²]Tridecan-3-yl]acetate belongs to the class of organic compounds known as indoles and derivatives. These are organic compounds containing an indole, which is a bicyclic ring system made up of a six-membered benzene ring fused to a five-membered nitrogen-containing pyrrole ring. Dendrine is found in Dendrobium nobile . Based on a literature review very few articles have been published on methyl 2-[(1S,3S,4S,7S,8S,11R,12R,13S)-2,12-dimethyl-9-oxo-13-(propan-2-yl)-10-oxa-2-azatetracyclo[5.4.1.1⁸,¹¹.0⁴,¹²]Tridecan-3-yl]acetate.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652304282210382D          

 24 27  0  0  1  0            999 V2000
    0.7510   -0.8748    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.8795   -0.0539    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.7597    0.1150    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.9747   -0.6188    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.2415   -1.2385    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.3667   -1.4789    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.8813   -2.1610    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0640   -1.9632    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.0326   -1.1266    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.4922   -0.4184    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0612    0.2168    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6319   -2.5218    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4514   -2.3353    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0122   -2.9404    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6950   -1.5471    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4994   -1.3639    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3868   -2.9005    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9352   -0.6668    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6220    0.1522    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0948    0.9080    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1609   -0.8957    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6392   -1.6305    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2781   -0.3940    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6641   -0.5830    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  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  1  6  1  0  0  0  0
  6  7  1  1  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  1  9  1  0  0  0  0
  9 10  1  1  0  0  0
 10 11  1  0  0  0  0
  2 11  1  1  0  0  0
  8 12  1  1  0  0  0
 12 13  1  0  0  0  0
 13 14  2  0  0  0  0
 13 15  1  0  0  0  0
 15 16  1  0  0  0  0
  7 17  1  0  0  0  0
  5 18  1  1  0  0  0
 18 19  1  0  0  0  0
  3 19  1  6  0  0  0
 19 20  2  0  0  0  0
  4 21  1  1  0  0  0
 21 22  1  0  0  0  0
 21 23  1  0  0  0  0
  1 24  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0064397

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC(=O)C[C@H]1[C@H]2CC[C@H]3[C@H]4[C@H](C(C)C)[C@@H](OC4=O)[C@@H](N1C)[C@@]23C

> <INCHI_IDENTIFIER>
InChI=1S/C19H29NO4/c1-9(2)14-15-11-7-6-10-12(8-13(21)23-5)20(4)17(19(10,11)3)16(14)24-18(15)22/h9-12,14-17H,6-8H2,1-5H3/t10-,11+,12+,14+,15+,16-,17-,19+/m1/s1

> <INCHI_KEY>
IAIIJNHQMKXPHL-JMMPBUAGSA-N

> <FORMULA>
C19H29NO4

> <MOLECULAR_WEIGHT>
335.444

> <EXACT_MASS>
335.209658418

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
53

> <JCHEM_AVERAGE_POLARIZABILITY>
27.583835835162283

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
methyl 2-[(1S,3S,4S,7S,8S,11R,12R,13S)-2,12-dimethyl-9-oxo-13-(propan-2-yl)-10-oxa-2-azatetracyclo[5.4.1.1^{8,11}.0^{4,12}]tridecan-3-yl]acetate

> <ALOGPS_LOGP>
2.66

> <JCHEM_LOGP>
2.276676600000001

> <ALOGPS_LOGS>
-2.64

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_BASIC>
9.480603475035409

> <JCHEM_POLAR_SURFACE_AREA>
55.84

> <JCHEM_REFRACTIVITY>
88.31209999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
7.71e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
methyl [(1S,3S,4S,7S,8S,11R,12R,13S)-13-isopropyl-2,12-dimethyl-9-oxo-10-oxa-2-azatetracyclo[5.4.1.1^{8,11}.0^{4,12}]tridecan-3-yl]acetate

> <JCHEM_VEBER_RULE>
0

$$$$

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       1.402  -1.633   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.642  -0.101   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       3.285   0.215   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       3.686  -1.155   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       4.184  -2.312   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.551  -2.761   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0       1.645  -4.034   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0       0.119  -3.665   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -0.061  -2.103   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -0.919  -0.781   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       0.114   0.405   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -1.179  -4.707   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -2.709  -4.359   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0      -3.756  -5.489   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0      -3.164  -2.888   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0      -4.666  -2.546   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       2.589  -5.414   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       5.479  -1.245   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0       4.894   0.284   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0       5.777   1.695   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0       2.167  -1.672   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       1.193  -3.044   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       0.519  -0.736   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       3.106  -1.088   0.000  0.00  0.00           C+0
CONECT    1    2    6    9   24                                             
CONECT    2    1    3   11                                                  
CONECT    3    2    4   19                                                  
CONECT    4    3    5   21                                                  
CONECT    5    4    6   18                                                  
CONECT    6    5    1    7                                                  
CONECT    7    6    8   17                                                  
CONECT    8    7    9   12                                                  
CONECT    9    8    1   10                                                  
CONECT   10    9   11                                                       
CONECT   11   10    2                                                       
CONECT   12    8   13                                                       
CONECT   13   12   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13   16                                                       
CONECT   16   15                                                            
CONECT   17    7                                                            
CONECT   18    5   19                                                       
CONECT   19   18    3   20                                                  
CONECT   20   19                                                            
CONECT   21    4   22   23                                                  
CONECT   22   21                                                            
CONECT   23   21                                                            
CONECT   24    1                                                            
MASTER        0    0    0    0    0    0    0    0   24    0   54    0
END

View in JSmol

Synonyms

Value	Source
Methyl 2-[(1S,3S,4S,7S,8S,11R,12R,13S)-2,12-dimethyl-9-oxo-13-(propan-2-yl)-10-oxa-2-azatetracyclo[5.4.1.1,.0,]tridecan-3-yl]acetic acid	Generator

Chemical Formula

C₁₉H₂₉NO₄

Average Mass

335.4440 Da

Monoisotopic Mass

335.20966 Da

IUPAC Name

methyl 2-[(1S,3S,4S,7S,8S,11R,12R,13S)-2,12-dimethyl-9-oxo-13-(propan-2-yl)-10-oxa-2-azatetracyclo[5.4.1.1^{8,11}.0^{4,12}]tridecan-3-yl]acetate

Traditional Name

methyl [(1S,3S,4S,7S,8S,11R,12R,13S)-13-isopropyl-2,12-dimethyl-9-oxo-10-oxa-2-azatetracyclo[5.4.1.1^{8,11}.0^{4,12}]tridecan-3-yl]acetate

CAS Registry Number

Not Available

SMILES

COC(=O)C[C@H]1[C@H]2CC[C@H]3[C@H]4[C@H](C(C)C)[C@@H](OC4=O)[C@@H](N1C)[C@@]23C

InChI Identifier

InChI=1S/C19H29NO4/c1-9(2)14-15-11-7-6-10-12(8-13(21)23-5)20(4)17(19(10,11)3)16(14)24-18(15)22/h9-12,14-17H,6-8H2,1-5H3/t10-,11+,12+,14+,15+,16-,17-,19+/m1/s1

InChI Key

IAIIJNHQMKXPHL-JMMPBUAGSA-N

Experimental Spectra

Not Available

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Dendrobium nobile	Plant	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as indoles and derivatives. These are organic compounds containing an indole, which is a bicyclic ring system made up of a six-membered benzene ring fused to a five-membered nitrogen-containing pyrrole ring.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Indoles and derivatives

Sub Class

Not Available

Direct Parent

Indoles and derivatives

Alternative Parents

Substituents

Indole or derivatives
Caprolactone
Oxepane
N-alkylpyrrolidine
Gamma butyrolactone
Dicarboxylic acid or derivatives
Methyl ester
Tetrahydrofuran
Pyrrolidine
Tertiary aliphatic amine
Tertiary amine
Lactone
Carboxylic acid ester
Amino acid or derivatives
Oxacycle
Azacycle
Carboxylic acid derivative
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Organonitrogen compound
Carbonyl group
Amine
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic 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	2.66	ALOGPS
logP	2.28	ChemAxon
logS	-2.6	ALOGPS
pKa (Strongest Basic)	9.48	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	55.84 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	88.31 m³·mol⁻¹	ChemAxon
Polarizability	27.58 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

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

154496456

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Dendrine (NP0064397)

MOL for NP0064397 (Dendrine)

3D MOL for NP0064397 (Dendrine)

3D SDF for NP0064397 (Dendrine)

3D-SDF for NP0064397 (Dendrine)

PDB for NP0064397 (Dendrine)

3D PDB for NP0064397 (Dendrine)

SMILES for NP0064397 (Dendrine)

INCHI for NP0064397 (Dendrine)

Structure for NP0064397 (Dendrine)

3D Structure for NP0064397 (Dendrine)