NP-MRD: Showing NP-Card for (1s,12s,15r,16s,17s,20s)-1,16,20-trimethyl-16-(4-methylpent-3-en-1-yl)-3-azapentacyclo[10.8.0.0²,¹⁰.0⁴,⁹.0¹⁵,²⁰]icosa-2(10),4,6,8-tetraen-17-ol (NP0207833)

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Record Information

Version

2.0

Created at

2022-09-05 04:36:17 UTC

Updated at

2022-09-05 04:36:17 UTC

NP-MRD ID

NP0207833

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(1s,12s,15r,16s,17s,20s)-1,16,20-trimethyl-16-(4-methylpent-3-en-1-yl)-3-azapentacyclo[10.8.0.0²,¹⁰.0⁴,⁹.0¹⁵,²⁰]icosa-2(10),4,6,8-tetraen-17-ol

Description

Emindole Sb belongs to the class of organic compounds known as diterpenoids. These are terpene compounds formed by four isoprene units. (1s,12s,15r,16s,17s,20s)-1,16,20-trimethyl-16-(4-methylpent-3-en-1-yl)-3-azapentacyclo[10.8.0.0²,¹⁰.0⁴,⁹.0¹⁵,²⁰]icosa-2(10),4,6,8-tetraen-17-ol is found in Albophoma yamanashiensis, Aspergillus oryzae, Aspergillus striatus and Penicillium thiersii. (1s,12s,15r,16s,17s,20s)-1,16,20-trimethyl-16-(4-methylpent-3-en-1-yl)-3-azapentacyclo[10.8.0.0²,¹⁰.0⁴,⁹.0¹⁵,²⁰]icosa-2(10),4,6,8-tetraen-17-ol was first documented in 2019 (PMID: 31188002). Based on a literature review a small amount of articles have been published on Emindole Sb (PMID: 33596652) (PMID: 34096406) (PMID: 33322052) (PMID: 31391888).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309052206362D          

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M  END

     RDKit          3D

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M  END


  Mrv1652309052206362D          

 30 34  0  0  1  0            999 V2000
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M  END
> <DATABASE_ID>
NP0207833

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(C)=CCC[C@]1(C)[C@@H](O)CC[C@@]2(C)[C@H]1CC[C@H]1CC3=C(NC4=CC=CC=C34)[C@]21C

> <INCHI_IDENTIFIER>
InChI=1S/C28H39NO/c1-18(2)9-8-15-26(3)23-13-12-19-17-21-20-10-6-7-11-22(20)29-25(21)28(19,5)27(23,4)16-14-24(26)30/h6-7,9-11,19,23-24,29-30H,8,12-17H2,1-5H3/t19-,23-,24-,26-,27-,28+/m0/s1

> <INCHI_KEY>
XOLHQUYGSUGTQA-DFGZTGKASA-N

> <FORMULA>
C28H39NO

> <MOLECULAR_WEIGHT>
405.626

> <EXACT_MASS>
405.30316488

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
69

> <JCHEM_AVERAGE_POLARIZABILITY>
50.58926393848074

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1S,12S,15R,16S,17S,20S)-1,16,20-trimethyl-16-(4-methylpent-3-en-1-yl)-3-azapentacyclo[10.8.0.0^{2,10}.0^{4,9}.0^{15,20}]icosa-2(10),4,6,8-tetraen-17-ol

> <JCHEM_LOGP>
6.614657378

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
19.896527425115977

> <JCHEM_PKA_STRONGEST_ACIDIC>
16.859192772253962

> <JCHEM_PKA_STRONGEST_BASIC>
-0.6570589042542706

> <JCHEM_POLAR_SURFACE_AREA>
36.019999999999996

> <JCHEM_REFRACTIVITY>
126.18919999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
(1S,12S,15R,16S,17S,20S)-1,16,20-trimethyl-16-(4-methylpent-3-en-1-yl)-3-azapentacyclo[10.8.0.0^{2,10}.0^{4,9}.0^{15,20}]icosa-2(10),4,6,8-tetraen-17-ol

> <JCHEM_VEBER_RULE>
1

$$$$

HEADER    PROTEIN                                 05-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   05-SEP-22         0                                  
HETATM    1  C   UNK     0      -3.043  -7.247   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -1.504  -7.308   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -0.682  -6.005   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -0.788  -8.671   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.751  -8.732   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.573  -7.429   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       3.112  -7.490   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       2.785  -8.995   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       2.905  -5.964   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       1.480  -5.381   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       4.123  -5.022   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       5.548  -5.605   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       5.755  -7.131   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       6.973  -6.189   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       4.537  -8.074   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       4.744  -9.600   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       6.170 -10.183   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       7.387  -9.241   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       8.903  -9.515   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       9.632  -8.159   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       8.567  -7.046   0.000  0.00  0.00           C+0
HETATM   22  N   UNK     0       9.297  -5.690   0.000  0.00  0.00           N+0
HETATM   23  C   UNK     0      10.812  -5.964   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      12.030  -5.022   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      13.455  -5.605   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      13.662  -7.131   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      12.445  -8.074   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      11.019  -7.490   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       7.180  -7.715   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       7.612  -6.236   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8    9   15                                             
CONECT    8    7                                                            
CONECT    9    7   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14   15   29                                             
CONECT   14   13                                                            
CONECT   15   13    7   16                                                  
CONECT   16   15   17                                                       
CONECT   17   16   18                                                       
CONECT   18   17   19   29                                                  
CONECT   19   18   20                                                       
CONECT   20   19   21   28                                                  
CONECT   21   20   22   29                                                  
CONECT   22   21   23                                                       
CONECT   23   22   24   28                                                  
CONECT   24   23   25                                                       
CONECT   25   24   26                                                       
CONECT   26   25   27                                                       
CONECT   27   26   28                                                       
CONECT   28   27   20   23                                                  
CONECT   29   21   18   13   30                                             
CONECT   30   29                                                            
MASTER        0    0    0    0    0    0    0    0   30    0   68    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₈H₃₉NO

Average Mass

405.6260 Da

Monoisotopic Mass

405.30316 Da

IUPAC Name

(1S,12S,15R,16S,17S,20S)-1,16,20-trimethyl-16-(4-methylpent-3-en-1-yl)-3-azapentacyclo[10.8.0.0^{2,10}.0^{4,9}.0^{15,20}]icosa-2(10),4,6,8-tetraen-17-ol

Traditional Name

(1S,12S,15R,16S,17S,20S)-1,16,20-trimethyl-16-(4-methylpent-3-en-1-yl)-3-azapentacyclo[10.8.0.0^{2,10}.0^{4,9}.0^{15,20}]icosa-2(10),4,6,8-tetraen-17-ol

CAS Registry Number

Not Available

SMILES

CC(C)=CCC[C@]1(C)[C@@H](O)CC[C@@]2(C)[C@H]1CC[C@H]1CC3=C(NC4=CC=CC=C34)[C@]21C

InChI Identifier

InChI=1S/C28H39NO/c1-18(2)9-8-15-26(3)23-13-12-19-17-21-20-10-6-7-11-22(20)29-25(21)28(19,5)27(23,4)16-14-24(26)30/h6-7,9-11,19,23-24,29-30H,8,12-17H2,1-5H3/t19-,23-,24-,26-,27-,28+/m0/s1

InChI Key

XOLHQUYGSUGTQA-DFGZTGKASA-N

Experimental Spectra

Not Available

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 25 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Albophoma yamanashiensis	LOTUS Database	35616633
Aspergillus oryzae	LOTUS Database	35616633
Emericella striata	LOTUS Database	35616633
Penicillium thiersii	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as diterpenoids. These are terpene compounds formed by four isoprene units.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Diterpenoids

Direct Parent

Diterpenoids

Alternative Parents

Substituents

Diterpenoid
3-alkylindole
Indole
Indole or derivatives
Benzenoid
Cyclic alcohol
Heteroaromatic compound
Pyrrole
Secondary alcohol
Azacycle
Organoheterocyclic compound
Alcohol
Organooxygen compound
Organonitrogen compound
Hydrocarbon derivative
Organopnictogen compound
Organic oxygen compound
Organic nitrogen compound
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	6.61	ChemAxon
pKa (Strongest Acidic)	16.86	ChemAxon
pKa (Strongest Basic)	-0.66	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	1	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	36.02 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	126.19 m³·mol⁻¹	ChemAxon
Polarizability	50.59 Å³	ChemAxon
Number of Rings	5	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	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

C00051940

Chemspider ID

8063240

KEGG Compound ID

C20527

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

9887568

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Kong FD, Fan P, Zhou LM, Ma QY, Xie QY, Zheng HZ, Zheng ZH, Zhang RS, Yuan JZ, Dai HF, Luo DQ, Zhao YX: Penerpenes A-D, Four Indole Terpenoids with Potent Protein Tyrosine Phosphatase Inhibitory Activity from the Marine-Derived Fungus Penicillium sp. KFD28. Org Lett. 2019 Jun 21;21(12):4864-4867. doi: 10.1021/acs.orglett.9b01751. Epub 2019 Jun 12. [PubMed:31188002 ]
Thomas WP, Pronin SV: New Methods and Strategies in the Synthesis of Terpenoid Natural Products. Acc Chem Res. 2021 Mar 16;54(6):1347-1359. doi: 10.1021/acs.accounts.0c00809. Epub 2021 Feb 17. [PubMed:33596652 ]
Chaiyosang B, Kanokmedhakul K, Yodsing N, Boonlue S, Yang JX, Wang YA, Andersen RJ, Yahuafai J, Kanokmedhakul S: Three new indole diterpenoids from Aspergillus aculeatus KKU-CT2. Nat Prod Res. 2022 Oct;36(19):4973-4981. doi: 10.1080/14786419.2021.1914613. Epub 2021 Jun 6. [PubMed:34096406 ]
Gaudencio SP, Pereira F: A Computer-Aided Drug Design Approach to Predict Marine Drug-Like Leads for SARS-CoV-2 Main Protease Inhibition. Mar Drugs. 2020 Dec 10;18(12):633. doi: 10.3390/md18120633. [PubMed:33322052 ]
Van de Bittner KC, Cameron RC, Bustamante LY, Bundela R, Kessans SA, Vorster J, Nicholson MJ, Parker EJ: Nodulisporic acid E biosynthesis: in vivo characterisation of NodD1, an indole-diterpene prenyltransferase that acts on an emindole SB derived indole-diterpene scaffold. Medchemcomm. 2019 May 27;10(7):1160-1164. doi: 10.1039/c9md00143c. eCollection 2019 Jul 1. [PubMed:31391888 ]
LOTUS database [Link]

Showing NP-Card for (1s,12s,15r,16s,17s,20s)-1,16,20-trimethyl-16-(4-methylpent-3-en-1-yl)-3-azapentacyclo[10.8.0.0²,¹⁰.0⁴,⁹.0¹⁵,²⁰]icosa-2(10),4,6,8-tetraen-17-ol (NP0207833)

MOL for NP0207833 ((1s,12s,15r,16s,17s,20s)-1,16,20-trimethyl-16-(4-methylpent-3-en-1-yl)-3-azapentacyclo[10.8.0.0²,¹⁰.0⁴,⁹.0¹⁵,²⁰]icosa-2(10),4,6,8-tetraen-17-ol)

3D MOL for NP0207833 ((1s,12s,15r,16s,17s,20s)-1,16,20-trimethyl-16-(4-methylpent-3-en-1-yl)-3-azapentacyclo[10.8.0.0²,¹⁰.0⁴,⁹.0¹⁵,²⁰]icosa-2(10),4,6,8-tetraen-17-ol)

3D SDF for NP0207833 ((1s,12s,15r,16s,17s,20s)-1,16,20-trimethyl-16-(4-methylpent-3-en-1-yl)-3-azapentacyclo[10.8.0.0²,¹⁰.0⁴,⁹.0¹⁵,²⁰]icosa-2(10),4,6,8-tetraen-17-ol)

3D-SDF for NP0207833 ((1s,12s,15r,16s,17s,20s)-1,16,20-trimethyl-16-(4-methylpent-3-en-1-yl)-3-azapentacyclo[10.8.0.0²,¹⁰.0⁴,⁹.0¹⁵,²⁰]icosa-2(10),4,6,8-tetraen-17-ol)

PDB for NP0207833 ((1s,12s,15r,16s,17s,20s)-1,16,20-trimethyl-16-(4-methylpent-3-en-1-yl)-3-azapentacyclo[10.8.0.0²,¹⁰.0⁴,⁹.0¹⁵,²⁰]icosa-2(10),4,6,8-tetraen-17-ol)

3D PDB for NP0207833 ((1s,12s,15r,16s,17s,20s)-1,16,20-trimethyl-16-(4-methylpent-3-en-1-yl)-3-azapentacyclo[10.8.0.0²,¹⁰.0⁴,⁹.0¹⁵,²⁰]icosa-2(10),4,6,8-tetraen-17-ol)

SMILES for NP0207833 ((1s,12s,15r,16s,17s,20s)-1,16,20-trimethyl-16-(4-methylpent-3-en-1-yl)-3-azapentacyclo[10.8.0.0²,¹⁰.0⁴,⁹.0¹⁵,²⁰]icosa-2(10),4,6,8-tetraen-17-ol)

INCHI for NP0207833 ((1s,12s,15r,16s,17s,20s)-1,16,20-trimethyl-16-(4-methylpent-3-en-1-yl)-3-azapentacyclo[10.8.0.0²,¹⁰.0⁴,⁹.0¹⁵,²⁰]icosa-2(10),4,6,8-tetraen-17-ol)

Structure for NP0207833 ((1s,12s,15r,16s,17s,20s)-1,16,20-trimethyl-16-(4-methylpent-3-en-1-yl)-3-azapentacyclo[10.8.0.0²,¹⁰.0⁴,⁹.0¹⁵,²⁰]icosa-2(10),4,6,8-tetraen-17-ol)

3D Structure for NP0207833 ((1s,12s,15r,16s,17s,20s)-1,16,20-trimethyl-16-(4-methylpent-3-en-1-yl)-3-azapentacyclo[10.8.0.0²,¹⁰.0⁴,⁹.0¹⁵,²⁰]icosa-2(10),4,6,8-tetraen-17-ol)