NP-MRD: Showing NP-Card for (±)-Penindolene D (NP0332840)

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Record Information

Version

2.0

Created at

2024-04-23 06:09:12 UTC

Updated at

2024-09-03 04:20:26 UTC

NP-MRD ID

NP0332840

Natural Product DOI

https://doi.org/10.57994/2115

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(±)-Penindolene D

Description

(±)-Penindolene D belongs to the class of organic compounds known as indoles. Indoles are compounds containing an indole moiety, which consists of pyrrole ring fused to benzene to form 2,3-benzopyrrole. (±)-Penindolene D was first documented in 2024 (PMID: 38635317). Based on a literature review very few articles have been published on (±)-Penindolene D.

Structure

MOL SDF PDB SMILES InChI


  Mrv2104 01052308462D          

 24 26  0  0  1  0            999 V2000
   -0.1712   -1.5229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1712   -0.6979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1712    0.1271    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9962   -0.6979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4087   -1.4124    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6538   -0.6979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387   -0.0305    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8838    0.7541    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0768    0.9256    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1781    1.7103    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9628    1.9652    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.6302    1.4803    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5440    0.6598    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9628    2.7902    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1781    3.0451    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3068    2.3777    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1318    2.3777    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233   -0.2854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    0.1271    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523   -0.2854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523   -1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378   -1.5229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233   -1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387   -1.3654    0.0000 N   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
  2  4  1  0  0  0  0
  4  5  2  0  0  0  0
  2  6  1  0  0  0  0
  6  7  2  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 11 10  1  0  0  0  0
 11 12  1  1  0  0  0
 12 13  1  0  0  0  0
 11 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 10 16  1  0  0  0  0
 16 17  2  0  0  0  0
  7 18  1  0  0  0  0
 18 19  2  0  0  0  0
 19 20  1  0  0  0  0
 20 21  2  0  0  0  0
 21 22  1  0  0  0  0
 22 23  2  0  0  0  0
 18 23  1  0  0  0  0
 23 24  1  0  0  0  0
  6 24  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0332840

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CO[C@H]1CCC(=O)N1CCC1=C(NC2=CC=CC=C12)C(C)(C)C=C

> <INCHI_IDENTIFIER>
InChI=1S/C20H26N2O2/c1-5-20(2,3)19-15(14-8-6-7-9-16(14)21-19)12-13-22-17(23)10-11-18(22)24-4/h5-9,18,21H,1,10-13H2,2-4H3/t18-/m0/s1

> <INCHI_KEY>
PPTBZGNWERYEIM-SFHVURJKSA-N

> <FORMULA>
C20H26N2O2

> <MOLECULAR_WEIGHT>
326.44

> <EXACT_MASS>
326.199428085

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
50

> <JCHEM_AVERAGE_POLARIZABILITY>
37.371501855137275

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(5S)-5-methoxy-1-{2-[2-(2-methylbut-3-en-2-yl)-1H-indol-3-yl]ethyl}pyrrolidin-2-one

> <JCHEM_LOGP>
3.411802251666666

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
15.496873682171238

> <JCHEM_PKA_STRONGEST_BASIC>
-1.9025642436908752

> <JCHEM_POLAR_SURFACE_AREA>
45.33

> <JCHEM_REFRACTIVITY>
96.68870000000003

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(5S)-5-methoxy-1-{2-[2-(2-methylbut-3-en-2-yl)-1H-indol-3-yl]ethyl}pyrrolidin-2-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 05-JAN-23   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   05-JAN-23         0                                  
HETATM    1  C   UNK     0      -0.320  -2.843   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -0.320  -1.303   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -0.320   0.237   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -1.860  -1.303   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -2.630  -2.637   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.220  -1.303   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       2.126  -0.057   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       1.650   1.408   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       0.143   1.728   0.000  0.00  0.00           C+0
HETATM   10  N   UNK     0      -0.333   3.192   0.000  0.00  0.00           N+0
HETATM   11  C   UNK     0      -1.797   3.668   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0      -3.043   2.763   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0      -2.882   1.232   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -1.797   5.208   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -0.333   5.684   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       0.573   4.438   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0       2.113   4.438   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0       3.590  -0.533   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       4.924   0.237   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       6.258  -0.533   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       6.258  -2.073   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       4.924  -2.843   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       3.590  -2.073   0.000  0.00  0.00           C+0
HETATM   24  N   UNK     0       2.126  -2.549   0.000  0.00  0.00           N+0
CONECT    1    2                                                            
CONECT    2    1    3    4    6                                             
CONECT    3    2                                                            
CONECT    4    2    5                                                       
CONECT    5    4                                                            
CONECT    6    2    7   24                                                  
CONECT    7    6    8   18                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11   16                                                  
CONECT   11   10   12   14                                                  
CONECT   12   11   13                                                       
CONECT   13   12                                                            
CONECT   14   11   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15   10   17                                                  
CONECT   17   16                                                            
CONECT   18    7   19   23                                                  
CONECT   19   18   20                                                       
CONECT   20   19   21                                                       
CONECT   21   20   22                                                       
CONECT   22   21   23                                                       
CONECT   23   22   18   24                                                  
CONECT   24   23    6                                                       
MASTER        0    0    0    0    0    0    0    0   24    0   52    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₀H₂₆N₂O₂

Average Mass

326.4400 Da

Monoisotopic Mass

326.19943 Da

IUPAC Name

(5S)-5-methoxy-1-{2-[2-(2-methylbut-3-en-2-yl)-1H-indol-3-yl]ethyl}pyrrolidin-2-one

Traditional Name

(5S)-5-methoxy-1-{2-[2-(2-methylbut-3-en-2-yl)-1H-indol-3-yl]ethyl}pyrrolidin-2-one

CAS Registry Number

Not Available

SMILES

CO[C@H]1CCC(=O)N1CCC1=C(NC2=CC=CC=C12)C(C)(C)C=C

InChI Identifier

InChI=1S/C20H26N2O2/c1-5-20(2,3)19-15(14-8-6-7-9-16(14)21-19)12-13-22-17(23)10-11-18(22)24-4/h5-9,18,21H,1,10-13H2,2-4H3/t18-/m0/s1

InChI Key

PPTBZGNWERYEIM-SFHVURJKSA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
COSY NMR	[¹H, ¹H] NMR Spectrum (2D, 500 MHz, C2D6OS, experimental)	m8545303@163.com	Institute of Oceanology, Chinese Academy of Sciences	Linghong Meng	2024-04-23	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, C3D6O, experimental)	m8545303@163.com	Institute of Oceanology, Chinese Academy of Sciences	Linghong Meng	2024-04-23	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, C2D6OS, experimental)	m8545303@163.com	Institute of Oceanology, Chinese Academy of Sciences	Linghong Meng	2024-04-23	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, C2D6OS, experimental)	m8545303@163.com	Institute of Oceanology, Chinese Academy of Sciences	Linghong Meng	2024-04-23	View Spectrum
HSQC NMR	[¹H, ¹³C] NMR Spectrum (2D, 500 MHz, CDCl3, experimental)	m8545303@163.com	Institute of Oceanology, Chinese Academy of Sciences	Linghong Meng	2024-04-23	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, C2D6OS, experimental)	m8545303@163.com	Institute of Oceanology, Chinese Academy of Sciences	Linghong Meng	2024-04-23	View Spectrum
HMBC NMR	[¹H, ¹³C] NMR Spectrum (2D, 500 MHz, C2D6OS, experimental)	m8545303@163.com	Institute of Oceanology, Chinese Academy of Sciences	Linghong Meng	2024-04-23	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
brocae MA-231		Not Available

Chemical Taxonomy

Description

This compound belongs to the class of organic compounds known as indoles. These are compounds containing an indole moiety, which consists of pyrrole ring fused to benzene to form 2,3-benzopyrrole.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Indoles and derivatives

Sub Class

Indoles

Direct Parent

Indoles

Alternative Parents

Substituents

Indole
Benzenoid
N-alkylpyrrolidine
2-pyrrolidone
Pyrrolidone
Heteroaromatic compound
Tertiary carboxylic acid amide
Pyrroline
Pyrrolidine
Pyrrole
Lactam
Carboxamide group
Amino acid or derivatives
Azacycle
Secondary amine
Secondary aliphatic amine
Carboxylic acid derivative
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Organonitrogen 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	3.41	ChemAxon
pKa (Strongest Acidic)	15.5	ChemAxon
pKa (Strongest Basic)	-1.9	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	2	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	45.33 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	96.69 m³·mol⁻¹	ChemAxon
Polarizability	37.37 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	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

Meng LH, Awakawa T, Li XM, Quan Z, Yang SQ, Wang BG, Abe I: Discovery of (+/-)-Penindolenes Reveals an Unusual Indole Ring Cleavage Pathway Catalyzed by P450 Monooxygenase. Angew Chem Int Ed Engl. 2024 Apr 18:e202403963. doi: 10.1002/anie.202403963. [PubMed:38635317 ]

Showing NP-Card for (±)-Penindolene D (NP0332840)

MOL for NP0332840 ((±)-Penindolene D)

3D MOL for NP0332840 ((±)-Penindolene D)

3D SDF for NP0332840 ((±)-Penindolene D)

3D-SDF for NP0332840 ((±)-Penindolene D)

PDB for NP0332840 ((±)-Penindolene D)

3D PDB for NP0332840 ((±)-Penindolene D)

SMILES for NP0332840 ((±)-Penindolene D)

INCHI for NP0332840 ((±)-Penindolene D)

Structure for NP0332840 ((±)-Penindolene D)

3D Structure for NP0332840 ((±)-Penindolene D)