NP-MRD: Showing NP-Card for (+)-cyclopentanecarboxylic acid (NP0062273)

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Record Information

Version

2.0

Created at

2022-04-28 06:57:12 UTC

Updated at

2022-04-28 06:57:12 UTC

NP-MRD ID

NP0062273

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(+)-cyclopentanecarboxylic acid

Description

Xanthocidin belongs to the class of organic compounds known as cyclopentanols. Cyclopentanols are compounds containing a cyclopentane ring that carries an alcohol group. (+)-cyclopentanecarboxylic acid is found in Streptomyces sp. No.51-4. (+)-cyclopentanecarboxylic acid was first documented in 2014 (PMID: 24492731). Based on a literature review a small amount of articles have been published on Xanthocidin (PMID: 30533708) (PMID: 30300957).

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 32 32  0  0  0  0  0  0  0  0999 V2000
   -0.7738    1.8808    2.0761 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8714    1.3050    0.9088 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0228    0.4523    0.5355 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1980    0.4597    0.9692 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5093   -0.4726   -0.5095 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.9165   -1.8378   -0.1868 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1838   -0.0771   -1.6912 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0602   -0.1735   -0.6784 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.2499   -0.2202   -2.0403 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8911   -1.0570    0.0027 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.7578   -1.1700    1.4855 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3237   -0.8027   -0.4227 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0300    1.2816   -0.3008 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.2373    1.9302   -0.2712 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7244    2.4032    0.7682 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0013    2.0668   -1.4191 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0725    2.4964    2.3036 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5194    1.7708    2.8517 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1757   -2.4917    0.2939 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2467   -2.3948   -1.1146 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8111   -1.8684    0.4768 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9537   -0.7397   -2.4072 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3842    0.6522   -2.4527 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7087   -2.0996   -0.4012 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2288   -0.9603    1.8806 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4903   -0.4789    1.9595 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0458   -2.1921    1.8698 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8293   -0.0331    0.1431 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3260   -0.6565   -1.5317 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9288   -1.7444   -0.2723 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6937    1.7771   -1.0911 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2240    2.9942   -1.7337 H   0  0  0  0  0  0  0  0  0  0  0  0
 11 10  1  0
 10 12  1  0
 10  8  1  0
  8  9  1  6
  8 13  1  0
 13 14  1  0
 14 16  1  0
 14 15  2  0
 13  2  1  0
  2  1  2  3
  2  3  1  0
  3  4  2  0
  3  5  1  0
  5  6  1  0
  5  7  1  6
  5  8  1  0
 11 25  1  0
 11 26  1  0
 11 27  1  0
 10 24  1  6
 12 28  1  0
 12 29  1  0
 12 30  1  0
  9 23  1  0
 13 31  1  6
 16 32  1  0
  1 17  1  0
  1 18  1  0
  6 19  1  0
  6 20  1  0
  6 21  1  0
  7 22  1  0
M  END


  Mrv1652304282208572D          

 16 16  0  0  1  0            999 V2000
    0.9803   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4652   -0.8227    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1553   -0.1553    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.0997    0.6294    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.5678    1.1143    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.2352    0.6294    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0198    0.8843    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1628    1.8330    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9728    1.8330    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9084    0.4663    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6581    1.2366    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4632    1.0567    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4114    2.0239    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3297   -0.8227    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1501   -0.7365    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0059   -1.5764    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  1  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  2  0  0  0  0
  5  8  1  6  0  0  0
  5  9  1  1  0  0  0
  4 10  1  6  0  0  0
  4 11  1  1  0  0  0
 11 12  1  0  0  0  0
 11 13  1  0  0  0  0
  3 14  1  1  0  0  0
 14 15  2  0  0  0  0
 14 16  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0062273

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C11H16O5/c1-5(2)11(16)7(9(13)14)6(3)8(12)10(11,4)15/h5,7,15-16H,3H2,1-2,4H3,(H,13,14)/t7-,10+,11-/m0/s1

> <INCHI_KEY>
PBMOSPVYISYWDG-XROYCOCOSA-N

> <FORMULA>
C11H16O5

> <MOLECULAR_WEIGHT>
228.244

> <EXACT_MASS>
228.099773615

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
32

> <JCHEM_AVERAGE_POLARIZABILITY>
22.37493422846942

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(1R,2S,3S)-2,3-dihydroxy-3-methyl-5-methylidene-4-oxo-2-(propan-2-yl)cyclopentane-1-carboxylic acid

> <ALOGPS_LOGP>
0.18

> <JCHEM_LOGP>
0.5284534703333338

> <ALOGPS_LOGS>
-1.09

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
12.112031790062916

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.153642622800794

> <JCHEM_PKA_STRONGEST_BASIC>
-3.7521982921057537

> <JCHEM_POLAR_SURFACE_AREA>
94.83

> <JCHEM_REFRACTIVITY>
55.311

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.87e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1R,2S,3S)-2,3-dihydroxy-2-isopropyl-3-methyl-5-methylidene-4-oxocyclopentane-1-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       1.830  -0.290   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.735  -1.536   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.290  -0.290   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -0.186   1.175   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.060   2.080   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.306   1.175   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       3.770   1.651   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       0.304   3.422   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       1.816   3.422   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      -1.696   0.870   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0      -1.228   2.308   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -2.731   1.972   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -0.768   3.778   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -0.615  -1.536   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0      -2.147  -1.375   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0       0.011  -2.943   0.000  0.00  0.00           O+0
CONECT    1    2    3    6                                                  
CONECT    2    1                                                            
CONECT    3    1    4   14                                                  
CONECT    4    3    5   10   11                                             
CONECT    5    4    6    8    9                                             
CONECT    6    5    1    7                                                  
CONECT    7    6                                                            
CONECT    8    5                                                            
CONECT    9    5                                                            
CONECT   10    4                                                            
CONECT   11    4   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11                                                            
CONECT   14    3   15   16                                                  
CONECT   15   14                                                            
CONECT   16   14                                                            
MASTER        0    0    0    0    0    0    0    0   16    0   32    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₁H₁₆O₅

Average Mass

228.2440 Da

Monoisotopic Mass

228.09977 Da

IUPAC Name

(1R,2S,3S)-2,3-dihydroxy-3-methyl-5-methylidene-4-oxo-2-(propan-2-yl)cyclopentane-1-carboxylic acid

Traditional Name

(1R,2S,3S)-2,3-dihydroxy-2-isopropyl-3-methyl-5-methylidene-4-oxocyclopentane-1-carboxylic acid

CAS Registry Number

Not Available

SMILES

CC(C)[C@]1(O)[C@H](C(O)=O)C(=C)C(=O)[C@@]1(C)O

InChI Identifier

InChI=1S/C11H16O5/c1-5(2)11(16)7(9(13)14)6(3)8(12)10(11,4)15/h5,7,15-16H,3H2,1-2,4H3,(H,13,14)/t7-,10+,11-/m0/s1

InChI Key

PBMOSPVYISYWDG-XROYCOCOSA-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 sp. No.51-4	Bacteria	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as cyclopentanols. Cyclopentanols are compounds containing a cyclopentane ring that carries an alcohol group.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Alcohols and polyols

Direct Parent

Cyclopentanols

Alternative Parents

Substituents

Cyclopentanol
Acyloin
Tertiary alcohol
Cyclic alcohol
Cyclic ketone
Ketone
1,2-diol
Monocarboxylic acid or derivatives
Carboxylic acid
Carboxylic acid derivative
Organic oxide
Hydrocarbon derivative
Carbonyl group
Aliphatic homomonocyclic compound

Molecular Framework

Aliphatic homomonocyclic 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	0.18	ALOGPS
logP	0.53	ChemAxon
logS	-1.1	ALOGPS
pKa (Strongest Acidic)	4.15	ChemAxon
pKa (Strongest Basic)	-3.8	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	94.83 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	55.31 m³·mol⁻¹	ChemAxon
Polarizability	22.37 Å³	ChemAxon
Number of Rings	1	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

C00018734

Chemspider ID

179035

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

206670

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Ortlieb N, Keilhofer N, Schrey SD, Gross H, Niedermeyer THJ: Draft Genome Sequence of the Xanthocidin-Producing Strain Streptomyces sp. AcE210, Isolated from a Root Nodule of Alnus glutinosa (L.). Microbiol Resour Announc. 2018 Oct 11;7(14). pii: MRA01190-18. doi: 10.1128/MRA.01190-18. eCollection 2018 Oct. [PubMed:30533708 ]
Ortlieb N, Bretzel K, Kulik A, Haas J, Ludeke S, Keilhofer N, Schrey SD, Gross H, Niedermeyer THJ: Xanthocidin Derivatives from the Endophytic Streptomyces sp. AcE210 Provide Insight into Xanthocidin Biosynthesis. Chembiochem. 2018 Dec 4;19(23):2472-2480. doi: 10.1002/cbic.201800467. Epub 2018 Nov 6. [PubMed:30300957 ]
Takeda S, Yaji K, Matsumoto K, Amamoto T, Shindo M, Aramaki H: Xanthocidin derivatives as topoisomerase IIalpha enzymatic inhibitors. Biol Pharm Bull. 2014;37(2):331-4. doi: 10.1248/bpb.b13-00757. [PubMed:24492731 ]

Showing NP-Card for (+)-cyclopentanecarboxylic acid (NP0062273)

MOL for NP0062273 ((+)-cyclopentanecarboxylic acid)

3D MOL for NP0062273 ((+)-cyclopentanecarboxylic acid)

3D SDF for NP0062273 ((+)-cyclopentanecarboxylic acid)

3D-SDF for NP0062273 ((+)-cyclopentanecarboxylic acid)

PDB for NP0062273 ((+)-cyclopentanecarboxylic acid)

3D PDB for NP0062273 ((+)-cyclopentanecarboxylic acid)

SMILES for NP0062273 ((+)-cyclopentanecarboxylic acid)

INCHI for NP0062273 ((+)-cyclopentanecarboxylic acid)

Structure for NP0062273 ((+)-cyclopentanecarboxylic acid)

3D Structure for NP0062273 ((+)-cyclopentanecarboxylic acid)