NP-MRD: Showing NP-Card for Pentalenic acid (NP0064757)

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Record Information

Version

2.0

Created at

2022-04-28 09:02:26 UTC

Updated at

2022-04-28 09:02:26 UTC

NP-MRD ID

NP0064757

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Pentalenic acid

Description

Pentalenic acid, also known as pentalenate, belongs to the class of organic compounds known as angular triquinanes. These are triquinane with a structure based on a [6.3.0.0^1,5] Undecane carbon skeleton. Pentalenic acid is found in Streptomyces spp. Pentalenic acid was first documented in 2004 (PMID: 15387599). Based on a literature review a small amount of articles have been published on pentalenic acid (PMID: 16755041) (PMID: 28744271) (PMID: 16681390) (PMID: 21081950).

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 40 42  0  0  0  0  0  0  0  0999 V2000
    0.7945   -2.8304   -0.3027 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7794   -1.5537   -1.1177 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.2015   -1.1134   -1.3289 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6014   -0.6623    0.0656 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3172   -0.2428    0.7513 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.3895    1.2244    0.9723 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1192    1.8439    2.0689 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7474    1.1796    2.9172 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1543    3.2390    2.2310 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7022    1.8067    0.0327 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0901    0.8534   -0.9218 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.3845    1.1492   -1.0263 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.7953    0.8120   -2.3103 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0423    0.3259    0.0332 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.2827    1.0790    1.3195 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3853   -0.1740   -0.4523 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0971   -0.8094    0.3455 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2179   -0.4620   -0.2591 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.2730   -2.6953    0.6820 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2634   -3.6690   -0.8378 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8153   -3.1756   -0.0659 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2274   -1.7159   -2.0556 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8374   -1.9744   -1.6542 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2418   -0.2691   -2.0419 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3064    0.1831   -0.0654 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0887   -1.4746    0.6444 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1335   -0.8098    1.6854 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6254    3.7618    1.4787 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6111    2.9051   -0.0101 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6156    0.9528   -1.8894 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6196    2.2276   -0.8721 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5810   -0.1115   -2.5557 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7971    2.0465    1.1387 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9771    0.4497    1.9263 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3595    1.1751    1.8949 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3825   -0.5058   -1.4908 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0782    0.7116   -0.3935 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7936   -0.9200    0.2580 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5047   -1.7060   -0.2037 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0734   -1.0515    1.4098 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6 10  2  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 12 14  1  0
 14 15  1  1
 14 16  1  0
 14 17  1  0
 18 17  1  1
  6  7  1  0
  7  9  1  0
  7  8  2  0
 18  2  1  0
 18  5  1  0
 18 11  1  0
  1 19  1  0
  1 20  1  0
  1 21  1  0
  2 22  1  6
  3 23  1  0
  3 24  1  0
  4 25  1  0
  4 26  1  0
  5 27  1  1
 10 29  1  0
 11 30  1  6
 12 31  1  1
 13 32  1  0
 15 33  1  0
 15 34  1  0
 15 35  1  0
 16 36  1  0
 16 37  1  0
 16 38  1  0
 17 39  1  0
 17 40  1  0
  9 28  1  0
M  END


  Mrv1652304282211022D          

 18 20  0  0  1  0            999 V2000
   -0.4506   -0.4506    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.1956   -1.2352    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6294   -1.2352    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8843   -0.4506    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.2169    0.0343    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.4718    0.8190    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2968    0.8190    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5517    0.0343    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.2192   -0.4506    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9642   -1.2352    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1392   -1.2352    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.6543   -1.9026    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7817    1.4864    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6022    1.4002    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4462    2.2401    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9458   -1.5786    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2905   -2.0547    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2352   -0.1956    0.0000 O   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
  4  3  1  1  0  0  0
  4  5  1  0  0  0  0
  1  5  1  0  0  0  0
  5  6  1  1  0  0  0
  6  7  2  0  0  0  0
  8  7  1  6  0  0  0
  4  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
  4 11  1  0  0  0  0
 11 12  1  1  0  0  0
  7 13  1  0  0  0  0
 13 14  2  0  0  0  0
 13 15  1  0  0  0  0
  2 16  1  0  0  0  0
  2 17  1  0  0  0  0
  1 18  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0064757

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@@H]1CC[C@H]2C(=C[C@@H]3[C@@H](O)C(C)(C)C[C@]123)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C15H22O3/c1-8-4-5-10-9(13(17)18)6-11-12(16)14(2,3)7-15(8,10)11/h6,8,10-12,16H,4-5,7H2,1-3H3,(H,17,18)/t8-,10+,11-,12-,15+/m1/s1

> <INCHI_KEY>
WBLTVUMJMJIOGQ-YCGCYHNXSA-N

> <FORMULA>
C15H22O3

> <MOLECULAR_WEIGHT>
250.338

> <EXACT_MASS>
250.156894568

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
40

> <JCHEM_AVERAGE_POLARIZABILITY>
27.67547371672416

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(1S,2R,5R,8S,9R)-9-hydroxy-2,10,10-trimethyltricyclo[6.3.0.0^{1,5}]undec-6-ene-6-carboxylic acid

> <ALOGPS_LOGP>
2.27

> <JCHEM_LOGP>
2.1399934483333336

> <ALOGPS_LOGS>
-2.62

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.769577314308872

> <JCHEM_PKA_STRONGEST_BASIC>
-0.5185788043931673

> <JCHEM_POLAR_SURFACE_AREA>
57.53

> <JCHEM_REFRACTIVITY>
68.8501

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.96e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1S,2R,5R,8S,9R)-9-hydroxy-2,10,10-trimethyltricyclo[6.3.0.0^{1,5}]undec-6-ene-6-carboxylic acid

> <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      -0.841  -0.841   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -0.365  -2.306   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.175  -2.306   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.651  -0.841   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.405   0.064   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.881   1.529   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       2.421   1.529   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       2.897   0.064   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       4.142  -0.841   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       3.667  -2.306   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       2.127  -2.306   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       1.221  -3.552   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       3.326   2.775   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0       4.857   2.614   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0       2.700   4.181   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0      -1.765  -2.947   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      -0.542  -3.835   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0      -2.306  -0.365   0.000  0.00  0.00           O+0
CONECT    1    2    5   18                                                  
CONECT    2    1    3   16   17                                             
CONECT    3    2    4                                                       
CONECT    4    3    5    8   11                                             
CONECT    5    4    1    6                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8   13                                                  
CONECT    8    7    4    9                                                  
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10    4   12                                                  
CONECT   12   11                                                            
CONECT   13    7   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13                                                            
CONECT   16    2                                                            
CONECT   17    2                                                            
CONECT   18    1                                                            
MASTER        0    0    0    0    0    0    0    0   18    0   40    0
END

View in JSmol

Synonyms

Value	Source
Pentalenate	Generator

Chemical Formula

C₁₅H₂₂O₃

Average Mass

250.3380 Da

Monoisotopic Mass

250.15689 Da

IUPAC Name

(1S,2R,5R,8S,9R)-9-hydroxy-2,10,10-trimethyltricyclo[6.3.0.0^{1,5}]undec-6-ene-6-carboxylic acid

Traditional Name

(1S,2R,5R,8S,9R)-9-hydroxy-2,10,10-trimethyltricyclo[6.3.0.0^{1,5}]undec-6-ene-6-carboxylic acid

CAS Registry Number

Not Available

SMILES

C[C@@H]1CC[C@H]2C(=C[C@@H]3[C@@H](O)C(C)(C)C[C@]123)C(O)=O

InChI Identifier

InChI=1S/C15H22O3/c1-8-4-5-10-9(13(17)18)6-11-12(16)14(2,3)7-15(8,10)11/h6,8,10-12,16H,4-5,7H2,1-3H3,(H,17,18)/t8-,10+,11-,12-,15+/m1/s1

InChI Key

WBLTVUMJMJIOGQ-YCGCYHNXSA-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, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, 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 spp.	Bacteria	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as angular triquinanes. These are triquinane with a structure based on a [6.3.0.0^1,5] Undecane carbon skeleton.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Sesquiterpenoids

Direct Parent

Angular triquinanes

Alternative Parents

Substituents

Angular triquinane sesquiterpenoid
Cyclic alcohol
Secondary alcohol
Monocarboxylic acid or derivatives
Carboxylic acid
Carboxylic acid derivative
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Carbonyl group
Alcohol
Aliphatic homopolycyclic compound

Molecular Framework

Aliphatic homopolycyclic compounds

External Descriptors

sesquiterpenoid (CHEBI:68665 )
5-hydroxy monocarboxylic acid (CHEBI:68665 )
carbotricyclic compound (CHEBI:68665 )

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	2.27	ALOGPS
logP	2.14	ChemAxon
logS	-2.6	ALOGPS
pKa (Strongest Acidic)	4.77	ChemAxon
pKa (Strongest Basic)	-0.52	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	57.53 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	68.85 m³·mol⁻¹	ChemAxon
Polarizability	27.68 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	No	ChemAxon

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

C00021800

Chemspider ID

9163908

KEGG Compound ID

Not Available

BioCyc ID

CPDMETA-13643

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

10988713

PDB ID

Not Available

ChEBI ID

68665

Good Scents ID

Not Available

References

General References

Ihara M: Syntheses of biologically active natural products and leading compounds for new pharmaceuticals employing effective construction of a polycyclic skeleton. Chem Pharm Bull (Tokyo). 2006 Jun;54(6):765-74. doi: 10.1248/cpb.54.765. [PubMed:16755041 ]
Wakefield J, Hassan HM, Jaspars M, Ebel R, Rateb ME: Dual Induction of New Microbial Secondary Metabolites by Fungal Bacterial Co-cultivation. Front Microbiol. 2017 Jul 11;8:1284. doi: 10.3389/fmicb.2017.01284. eCollection 2017. [PubMed:28744271 ]
Tetzlaff CN, You Z, Cane DE, Takamatsu S, Omura S, Ikeda H: A gene cluster for biosynthesis of the sesquiterpenoid antibiotic pentalenolactone in Streptomyces avermitilis. Biochemistry. 2006 May 16;45(19):6179-86. doi: 10.1021/bi060419n. [PubMed:16681390 ]
Takamatsu S, Xu LH, Fushinobu S, Shoun H, Komatsu M, Cane DE, Ikeda H: Pentalenic acid is a shunt metabolite in the biosynthesis of the pentalenolactone family of metabolites: hydroxylation of 1-deoxypentalenic acid mediated by CYP105D7 (SAV_7469) of Streptomyces avermitilis. J Antibiot (Tokyo). 2011 Jan;64(1):65-71. doi: 10.1038/ja.2010.135. Epub 2010 Nov 17. [PubMed:21081950 ]
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Showing NP-Card for Pentalenic acid (NP0064757)

MOL for NP0064757 (Pentalenic acid)

3D MOL for NP0064757 (Pentalenic acid)

3D SDF for NP0064757 (Pentalenic acid)

3D-SDF for NP0064757 (Pentalenic acid)

PDB for NP0064757 (Pentalenic acid)

3D PDB for NP0064757 (Pentalenic acid)

SMILES for NP0064757 (Pentalenic acid)

INCHI for NP0064757 (Pentalenic acid)

Structure for NP0064757 (Pentalenic acid)

3D Structure for NP0064757 (Pentalenic acid)