NP-MRD: Showing NP-Card for 2-[(2e,5e,7e,9r,10r,11e)-10-hydroxy-3,7,9,11-tetramethyltrideca-2,5,7,11-tetraen-1-yl]-5,6-dimethoxy-3-methylpyridin-4-ol (NP0177394)

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Record Information

Version

1.0

Created at

2022-09-03 15:13:40 UTC

Updated at

2022-09-03 15:13:40 UTC

NP-MRD ID

NP0177394

Secondary Accession Numbers

None

Natural Product Identification

Common Name

2-[(2e,5e,7e,9r,10r,11e)-10-hydroxy-3,7,9,11-tetramethyltrideca-2,5,7,11-tetraen-1-yl]-5,6-dimethoxy-3-methylpyridin-4-ol

Description

Piericidin A, also known as AR 054 or shaoguanmycin b, belongs to the class of organic compounds known as sesquiterpenoids. These are terpenes with three consecutive isoprene units. 2-[(2e,5e,7e,9r,10r,11e)-10-hydroxy-3,7,9,11-tetramethyltrideca-2,5,7,11-tetraen-1-yl]-5,6-dimethoxy-3-methylpyridin-4-ol is found in Streptomyces lividans. It was first documented in 2002 (PMID: 12400692). Piericidin A is a moderately basic compound (based on its pKa) (PMID: 16277503) (PMID: 16953619) (PMID: 17721005) (PMID: 17941090).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv0541 05301214372D          

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M  END

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  Mrv0541 05301214372D          

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M  END
> <DATABASE_ID>
NP0177394

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H]\C(C)=C(\C)[C@]([H])(O)[C@]([H])(C)C(\[H])=C(/C)\C(\[H])=C(/[H])C\C(C)=C(/[H])CC1=C(C)C(O)=C(OC)C(OC)=N1

> <INCHI_IDENTIFIER>
InChI=1S/C25H37NO4/c1-9-18(4)22(27)19(5)15-17(3)12-10-11-16(2)13-14-21-20(6)23(28)24(29-7)25(26-21)30-8/h9-10,12-13,15,19,22,27H,11,14H2,1-8H3,(H,26,28)/b12-10+,16-13+,17-15+,18-9+/t19-,22+/m1/s1

> <INCHI_KEY>
BBLGCDSLCDDALX-LKGBESRRSA-N

> <FORMULA>
C25H37NO4

> <MOLECULAR_WEIGHT>
415.5656

> <EXACT_MASS>
415.272258677

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_AVERAGE_POLARIZABILITY>
48.78049930978712

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
2-[(2E,5E,7E,9R,10R,11E)-10-hydroxy-3,7,9,11-tetramethyltrideca-2,5,7,11-tetraen-1-yl]-5,6-dimethoxy-3-methylpyridin-4-ol

> <ALOGPS_LOGP>
5.58

> <JCHEM_LOGP>
5.383264734000001

> <ALOGPS_LOGS>
-5.07

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
18.862929312145415

> <JCHEM_PKA_STRONGEST_ACIDIC>
10.905995676229109

> <JCHEM_PKA_STRONGEST_BASIC>
1.9356355965940542

> <JCHEM_POLAR_SURFACE_AREA>
71.81000000000002

> <JCHEM_REFRACTIVITY>
127.292

> <JCHEM_ROTATABLE_BOND_COUNT>
10

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
3.55e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-[(2E,5E,7E,9R,10R,11E)-10-hydroxy-3,7,9,11-tetramethyltrideca-2,5,7,11-tetraen-1-yl]-5,6-dimethoxy-3-methylpyridin-4-ol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 30-MAY-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   30-MAY-12         0                                  
HETATM    1  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       0.000   0.000   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       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   26  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   27  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   28  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   29  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   30  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   31  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   32  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   33  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   34  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   35  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   36  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   37  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
CONECT    1    9                                                            
CONECT    2   16                                                            
CONECT    3   17                                                            
CONECT    4   18                                                            
CONECT    5   19                                                            
CONECT    6   20                                                            
CONECT    7   29                                                            
CONECT    8   30                                                            
CONECT    9    1   18   31                                                  
CONECT   10   11   12   32                                                  
CONECT   11   10   16                                                       
CONECT   12   10   17   33                                                  
CONECT   13   14   16   34                                                  
CONECT   14   13   21                                                       
CONECT   15   17   19   35                                                  
CONECT   16    2   11   13                                                  
CONECT   17    3   12   15                                                  
CONECT   18    4    9   22                                                  
CONECT   19    5   15   22   36                                             
CONECT   20    6   21   23                                                  
CONECT   21   14   20   26                                                  
CONECT   22   18   19   27   37                                             
CONECT   23   20   24   28                                                  
CONECT   24   23   25   29                                                  
CONECT   25   24   26   30                                                  
CONECT   26   21   25                                                       
CONECT   27   22                                                            
CONECT   28   23                                                            
CONECT   29    7   24                                                       
CONECT   30    8   25                                                       
CONECT   31    9                                                            
CONECT   32   10                                                            
CONECT   33   12                                                            
CONECT   34   13                                                            
CONECT   35   15                                                            
CONECT   36   19                                                            
CONECT   37   22                                                            
MASTER        0    0    0    0    0    0    0    0   37    0   74    0
END

View in JSmol

Synonyms

Value	Source
(+)-Piericidin a1	ChEBI
2-[(2E,5E,7E,11E)-10R-Hydroxy-3,7,9R,11-tetramethyl-2,5,7,11-tridecatetraen-1-yl]-5,6-dimethoxy-3-methyl-4-pyridinol	ChEBI
2-[(2E,5E,7E,9R,10R,11E)-10-Hydroxy-3,7,9,11-tetramethyltrideca-2,5,7,11-tetraenyl]-5,6-dimethoxy-3-methyl-1H-pyridin-4-one	ChEBI
AR 054	ChEBI
Piericidin a1	ChEBI
Shaoguanmycin b	ChEBI
sn 198E	ChEBI
2-(10-Hydroxy-3,7,9,11-tetramethyl-2,4,7,11-tridecatetraenyl)-5,6-dimethoxy-3-methyl-4-pyridinol	MeSH

Chemical Formula

C₂₅H₃₇NO₄

Average Mass

415.5656 Da

Monoisotopic Mass

415.27226 Da

IUPAC Name

2-[(2E,5E,7E,9R,10R,11E)-10-hydroxy-3,7,9,11-tetramethyltrideca-2,5,7,11-tetraen-1-yl]-5,6-dimethoxy-3-methylpyridin-4-ol

Traditional Name

2-[(2E,5E,7E,9R,10R,11E)-10-hydroxy-3,7,9,11-tetramethyltrideca-2,5,7,11-tetraen-1-yl]-5,6-dimethoxy-3-methylpyridin-4-ol

CAS Registry Number

Not Available

SMILES

[H]\C(C)=C(\C)[C@]([H])(O)[C@]([H])(C)C(\[H])=C(/C)\C(\[H])=C(/[H])C\C(C)=C(/[H])CC1=C(C)C(O)=C(OC)C(OC)=N1

InChI Identifier

InChI=1S/C25H37NO4/c1-9-18(4)22(27)19(5)15-17(3)12-10-11-16(2)13-14-21-20(6)23(28)24(29-7)25(26-21)30-8/h9-10,12-13,15,19,22,27H,11,14H2,1-8H3,(H,26,28)/b12-10+,16-13+,17-15+,18-9+/t19-,22+/m1/s1

InChI Key

BBLGCDSLCDDALX-LKGBESRRSA-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
Streptomyces lividans	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as sesquiterpenoids. These are terpenes with three consecutive isoprene units.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Sesquiterpenoids

Direct Parent

Sesquiterpenoids

Alternative Parents

Substituents

Farsesane sesquiterpenoid
Sesquiterpenoid
Alkyl aryl ether
Dihydropyridine
Methylpyridine
Hydropyridine
Pyridine
Heteroaromatic compound
Vinylogous ester
Vinylogous amide
Cyclic ketone
Secondary alcohol
Ether
Azacycle
Organoheterocyclic compound
Alcohol
Hydrocarbon derivative
Organooxygen compound
Organonitrogen compound
Organic oxide
Organopnictogen compound
Organic oxygen compound
Organic nitrogen compound
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic 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	5.58	ALOGPS
logP	5.38	ChemAxon
logS	-5.1	ALOGPS
pKa (Strongest Acidic)	10.91	ChemAxon
pKa (Strongest Basic)	1.94	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	71.81 Å²	ChemAxon
Rotatable Bond Count	10	ChemAxon
Refractivity	127.29 m³·mol⁻¹	ChemAxon
Polarizability	48.78 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	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

CPD0-1233

BiGG ID

Not Available

Wikipedia Link

Piericidin A

METLIN ID

Not Available

PubChem Compound

6437838

PDB ID

Not Available

ChEBI ID

138511

Good Scents ID

Not Available

References

General References

Ikezawa N, Ifuku K, Endo T, Sato F: Inhibition of photosystem II of spinach by the respiration inhibitors piericidin A and thenoyltrifluoroacetone. Biosci Biotechnol Biochem. 2002 Sep;66(9):1925-9. doi: 10.1271/bbb.66.1925. [PubMed:12400692 ]
Schnermann MJ, Boger DL: Total synthesis of piericidin A1 and B1. J Am Chem Soc. 2005 Nov 16;127(45):15704-5. doi: 10.1021/ja055041f. [PubMed:16277503 ]
Schnermann MJ, Romero FA, Hwang I, Nakamaru-Ogiso E, Yagi T, Boger DL: Total synthesis of piericidin A1 and B1 and key analogues. J Am Chem Soc. 2006 Sep 13;128(36):11799-807. doi: 10.1021/ja0632862. [PubMed:16953619 ]
Ueda JY, Togashi T, Matukura S, Nagai A, Nakashima T, Komaki H, Anzai K, Harayama S, Doi T, Takahashi T, Natsume T, Kisu Y, Goshima N, Nomura N, Takagi M, Shin-Ya K: A novel nuclear export inhibitor JBIR-02, a new piericidin discovered from Streptomyces sp. ML55. J Antibiot (Tokyo). 2007 Jul;60(7):459-62. doi: 10.1038/ja.2007.59. [PubMed:17721005 ]
Hwang JH, Kim JY, Cha MR, Ryoo IJ, Choo SJ, Cho SM, Tsukumo Y, Tomida A, Shin-Ya K, Hwang YI, Yoo ID, Park HR: Etoposide-resistant HT-29 human colon carcinoma cells during glucose deprivation are sensitive to piericidin A, a GRP78 down-regulator. J Cell Physiol. 2008 Apr;215(1):243-50. doi: 10.1002/jcp.21308. [PubMed:17941090 ]
LOTUS database [Link]

Showing NP-Card for 2-[(2e,5e,7e,9r,10r,11e)-10-hydroxy-3,7,9,11-tetramethyltrideca-2,5,7,11-tetraen-1-yl]-5,6-dimethoxy-3-methylpyridin-4-ol (NP0177394)

MOL for NP0177394 (2-[(2e,5e,7e,9r,10r,11e)-10-hydroxy-3,7,9,11-tetramethyltrideca-2,5,7,11-tetraen-1-yl]-5,6-dimethoxy-3-methylpyridin-4-ol)

3D MOL for NP0177394 (2-[(2e,5e,7e,9r,10r,11e)-10-hydroxy-3,7,9,11-tetramethyltrideca-2,5,7,11-tetraen-1-yl]-5,6-dimethoxy-3-methylpyridin-4-ol)

3D SDF for NP0177394 (2-[(2e,5e,7e,9r,10r,11e)-10-hydroxy-3,7,9,11-tetramethyltrideca-2,5,7,11-tetraen-1-yl]-5,6-dimethoxy-3-methylpyridin-4-ol)

3D-SDF for NP0177394 (2-[(2e,5e,7e,9r,10r,11e)-10-hydroxy-3,7,9,11-tetramethyltrideca-2,5,7,11-tetraen-1-yl]-5,6-dimethoxy-3-methylpyridin-4-ol)

PDB for NP0177394 (2-[(2e,5e,7e,9r,10r,11e)-10-hydroxy-3,7,9,11-tetramethyltrideca-2,5,7,11-tetraen-1-yl]-5,6-dimethoxy-3-methylpyridin-4-ol)

3D PDB for NP0177394 (2-[(2e,5e,7e,9r,10r,11e)-10-hydroxy-3,7,9,11-tetramethyltrideca-2,5,7,11-tetraen-1-yl]-5,6-dimethoxy-3-methylpyridin-4-ol)

SMILES for NP0177394 (2-[(2e,5e,7e,9r,10r,11e)-10-hydroxy-3,7,9,11-tetramethyltrideca-2,5,7,11-tetraen-1-yl]-5,6-dimethoxy-3-methylpyridin-4-ol)

INCHI for NP0177394 (2-[(2e,5e,7e,9r,10r,11e)-10-hydroxy-3,7,9,11-tetramethyltrideca-2,5,7,11-tetraen-1-yl]-5,6-dimethoxy-3-methylpyridin-4-ol)

Structure for NP0177394 (2-[(2e,5e,7e,9r,10r,11e)-10-hydroxy-3,7,9,11-tetramethyltrideca-2,5,7,11-tetraen-1-yl]-5,6-dimethoxy-3-methylpyridin-4-ol)

3D Structure for NP0177394 (2-[(2e,5e,7e,9r,10r,11e)-10-hydroxy-3,7,9,11-tetramethyltrideca-2,5,7,11-tetraen-1-yl]-5,6-dimethoxy-3-methylpyridin-4-ol)