NP-MRD: Showing NP-Card for PSX 1 (NP0021496)

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Record Information

Version

2.0

Created at

2021-01-06 06:46:40 UTC

Updated at

2021-07-15 17:36:30 UTC

NP-MRD ID

NP0021496

Secondary Accession Numbers

None

Natural Product Identification

Common Name

PSX 1

Provided By

NPAtlas

Description

Botryodiplodin, also known as antibiotic PSX 1 or cytostipin, belongs to the class of organic compounds known as tetrahydrofurans. These are heterocyclic compounds containing a saturated, aliphatic, five-membered ring where a carbon is replaced by an oxygen. PSX 1 is found in Botryodiplodia theobromae, Macrophomina phaseolina, Penicillium, Penicillium carneoluteus, Penicillium roquefortii and Talaromyces stipitatus. PSX 1 was first documented in 2007 (PMID: 17628075). Based on a literature review very few articles have been published on Botryodiplodin (PMID: 24768282) (PMID: 26837531) (PMID: 33287215) (PMID: 32842542) (PMID: 31906290) (PMID: 31698804).

Structure

MOL 3D MOL SDF 3D SDF PDB SMILES InChI


  Mrv1652306242105163D          

 22 22  0  0  0  0            999 V2000
    2.7406   -0.1002   -0.5880 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3586    0.4417   -0.4525 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0358    1.3023   -1.2387 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4321   -0.0395    0.5792 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.2452   -1.5425    0.3203 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.7734   -1.5975   -0.5989 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6727   -0.6071   -0.3020 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.7680   -1.0665    0.3968 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9533    0.4655    0.4964 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.1561    1.8101   -0.1026 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4278    0.7683   -0.5049 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9151   -0.5137   -1.6230 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9487   -0.8955    0.1275 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8977    0.0339    1.5880 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1567   -1.9564   -0.1415 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0429   -2.0581    1.2500 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0443   -0.1310   -1.2400 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5922   -1.3123    1.3285 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3819    0.4651    1.5399 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2507    1.7574   -1.2067 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1504    2.2248    0.2398 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3724    2.5511    0.1323 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  2  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  7  9  1  0  0  0  0
  9 10  1  0  0  0  0
  9  4  1  0  0  0  0
  1 11  1  0  0  0  0
  1 12  1  0  0  0  0
  1 13  1  0  0  0  0
  4 14  1  1  0  0  0
  5 15  1  0  0  0  0
  5 16  1  0  0  0  0
  7 17  1  6  0  0  0
  8 18  1  0  0  0  0
  9 19  1  1  0  0  0
 10 20  1  0  0  0  0
 10 21  1  0  0  0  0
 10 22  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0021496

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C7H12O3/c1-4-6(5(2)8)3-10-7(4)9/h4,6-7,9H,3H2,1-2H3/t4-,6-,7-/m1/s1

> <INCHI_KEY>
CLYSZQBIUYRLNX-UHFFFAOYSA-N

> <FORMULA>
C7H12O3

> <MOLECULAR_WEIGHT>
144.1684

> <EXACT_MASS>
144.07864425

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
22

> <JCHEM_AVERAGE_POLARIZABILITY>
14.540266245776149

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
1-[(3S,4R,5R)-5-hydroxy-4-methyloxolan-3-yl]ethan-1-one

> <ALOGPS_LOGP>
-0.52

> <JCHEM_LOGP>
0.1250225493333336

> <ALOGPS_LOGS>
0.37

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
17.06483815265755

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.169172435640048

> <JCHEM_PKA_STRONGEST_BASIC>
-4.036989169460296

> <JCHEM_POLAR_SURFACE_AREA>
46.53

> <JCHEM_REFRACTIVITY>
35.74719999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.38e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
1-[(3S,4R,5R)-5-hydroxy-4-methyloxolan-3-yl]ethanone

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 24-JUN-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-JUN-21         0                                  
HETATM    1  C   UNK     0       2.741  -0.100  -0.588  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.359   0.442  -0.453  0.00  0.00           C+0
HETATM    3  O   UNK     0       1.036   1.302  -1.239  0.00  0.00           O+0
HETATM    4  C   UNK     0       0.432  -0.040   0.579  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.245  -1.543   0.320  0.00  0.00           C+0
HETATM    6  O   UNK     0      -0.773  -1.597  -0.599  0.00  0.00           O+0
HETATM    7  C   UNK     0      -1.673  -0.607  -0.302  0.00  0.00           C+0
HETATM    8  O   UNK     0      -2.768  -1.067   0.397  0.00  0.00           O+0
HETATM    9  C   UNK     0      -0.953   0.466   0.496  0.00  0.00           C+0
HETATM   10  C   UNK     0      -1.156   1.810  -0.103  0.00  0.00           C+0
HETATM   11  H   UNK     0       3.428   0.768  -0.505  0.00  0.00           H+0
HETATM   12  H   UNK     0       2.915  -0.514  -1.623  0.00  0.00           H+0
HETATM   13  H   UNK     0       2.949  -0.896   0.128  0.00  0.00           H+0
HETATM   14  H   UNK     0       0.898   0.034   1.588  0.00  0.00           H+0
HETATM   15  H   UNK     0       1.157  -1.956  -0.142  0.00  0.00           H+0
HETATM   16  H   UNK     0      -0.043  -2.058   1.250  0.00  0.00           H+0
HETATM   17  H   UNK     0      -2.044  -0.131  -1.240  0.00  0.00           H+0
HETATM   18  H   UNK     0      -2.592  -1.312   1.329  0.00  0.00           H+0
HETATM   19  H   UNK     0      -1.382   0.465   1.540  0.00  0.00           H+0
HETATM   20  H   UNK     0      -1.251   1.757  -1.207  0.00  0.00           H+0
HETATM   21  H   UNK     0      -2.150   2.225   0.240  0.00  0.00           H+0
HETATM   22  H   UNK     0      -0.372   2.551   0.132  0.00  0.00           H+0
CONECT    1    2   11   12   13                                             
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5    9   14                                             
CONECT    5    4    6   15   16                                             
CONECT    6    5    7                                                       
CONECT    7    6    8    9   17                                             
CONECT    8    7   18                                                       
CONECT    9    7   10    4   19                                             
CONECT   10    9   20   21   22                                             
CONECT   11    1                                                            
CONECT   12    1                                                            
CONECT   13    1                                                            
CONECT   14    4                                                            
CONECT   15    5                                                            
CONECT   16    5                                                            
CONECT   17    7                                                            
CONECT   18    8                                                            
CONECT   19    9                                                            
CONECT   20   10                                                            
CONECT   21   10                                                            
CONECT   22   10                                                            
MASTER        0    0    0    0    0    0    0    0   22    0   44    0
END

View in JSmol View NMR Assignments

Synonyms

Value	Source
1-(Tetrahydro-5-hydroxy-4-methyl-3-furanyl)-ethanone	HMDB
1-(Tetrahydro-5-hydroxy-4-methyl-3-furanyl)ethanone	HMDB
1-(Tetrahydro-5-hydroxy-4-methyl-3-furanyl)ethanone, 9ci	HMDB
2-Hydroxy-3-methyl-4-acetyltetrahydrofuran	HMDB
2-Hydroxy-3-methyl-4-acetyltetrahydrofurane	HMDB
4-Acetyl-2-hydroxy-3-methyltetrahydrofuran	HMDB
Antibiotic PSX 1	HMDB
Botrydiplodin	HMDB
Botryodiplodin (synthetic)	HMDB
Botryodipolodin	HMDB
Botyrodiplodin	HMDB
Cytostipin	HMDB
Ketone, methyl tetrahydro-5-hydroxy-4-methyl-3-furyl	HMDB
Methyltetrahydro-5-hydroxy-4-methyl-3-furyl-ketone	HMDB
PSX 1	HMDB
Botriodiplodin	HMDB
PSX-1	HMDB
Botryodiplodin	MeSH

Chemical Formula

C₇H₁₂O₃

Average Mass

144.1684 Da

Monoisotopic Mass

144.07864 Da

IUPAC Name

1-[(3S,4R,5R)-5-hydroxy-4-methyloxolan-3-yl]ethan-1-one

Traditional Name

1-[(3S,4R,5R)-5-hydroxy-4-methyloxolan-3-yl]ethanone

CAS Registry Number

Not Available

SMILES

CC1C(O)OCC1C(C)=O

InChI Identifier

InChI=1S/C7H12O3/c1-4-6(5(2)8)3-10-7(4)9/h4,6-7,9H,3H2,1-2H3

InChI Key

CLYSZQBIUYRLNX-UHFFFAOYSA-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
Lasiodiplodia theobromae	Fungi	KNApSAcK
Macrophomina phaseolina	LOTUS Database	35616633
Penicillium	NPAtlas	4856962
Penicillium carneoluteus	Fungi	KNApSAcK
Penicillium roqueforti	Fungi	KNApSAcK
Talaromyces stipitatus	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as tetrahydrofurans. These are heterocyclic compounds containing a saturated, aliphatic, five-membered ring where a carbon is replaced by an oxygen.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Tetrahydrofurans

Sub Class

Not Available

Direct Parent

Tetrahydrofurans

Alternative Parents

Substituents

Tetrahydrofuran
Ketone
Hemiacetal
Oxacycle
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Carbonyl group
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic 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	-0.52	ALOGPS
logP	0.13	ChemAxon
logS	0.37	ALOGPS
pKa (Strongest Acidic)	12.17	ChemAxon
pKa (Strongest Basic)	-4	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	46.53 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	35.75 m³·mol⁻¹	ChemAxon
Polarizability	14.54 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

NPAtlas ID

NPA013308

HMDB ID

HMDB0036594

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB015506

KNApSAcK ID

C00054956

Chemspider ID

31076

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Botryodiplodin

METLIN ID

Not Available

PubChem Compound

33701

PDB ID

Not Available

ChEBI ID

168857

Good Scents ID

rw1482901

References

General References

Cabedo N, Lopez-Gresa MP, Primo J, Ciavatta ML, Gonzalez-Mas MC: Isolation and structural elucidation of eight new related analogues of the mycotoxin (-)-botryodiplodin from Penicillium coalescens. J Agric Food Chem. 2007 Aug 22;55(17):6977-83. doi: 10.1021/jf071568v. Epub 2007 Jul 12. [PubMed:17628075 ]
Andolfi A, Maddau L, Cimmino A, Linaldeddu BT, Basso S, Deidda A, Serra S, Evidente A: Lasiojasmonates A-C, three jasmonic acid esters produced by Lasiodiplodia sp., a grapevine pathogen. Phytochemistry. 2014 Jul;103:145-153. doi: 10.1016/j.phytochem.2014.03.016. Epub 2014 Apr 23. [PubMed:24768282 ]
Zang Y, Genta-Jouve G, Retailleau P, Escargueil A, Mann S, Nay B, Prado S: Talaroketals A and B, unusual bis(oxaphenalenone) spiro and fused ketals from the soil fungus Talaromyces stipitatus ATCC 10500. Org Biomol Chem. 2016 Mar 7;14(9):2691-7. doi: 10.1039/c5ob02657a. [PubMed:26837531 ]
Khambhati VH, Abbas HK, Sulyok M, Tomaso-Peterson M, Shier WT: First Report of the Production of Mycotoxins and Other Secondary Metabolites by Macrophomina phaseolina (Tassi) Goid. Isolates from Soybeans (Glycine max L.) Symptomatic with Charcoal Rot Disease. J Fungi (Basel). 2020 Dec 3;6(4). pii: jof6040332. doi: 10.3390/jof6040332. [PubMed:33287215 ]
Salvatore MM, Felix C, Lima F, Ferreira V, Duarte AS, Salvatore F, Alves A, Esteves AC, Andolfi A: Effect of gamma-Aminobutyric Acid (GABA) on the Metabolome of Two Strains of Lasiodiplodia theobromae Isolated from Grapevine. Molecules. 2020 Aug 23;25(17). pii: molecules25173833. doi: 10.3390/molecules25173833. [PubMed:32842542 ]
Abbas HK, Bellaloui N, Butler AM, Nelson JL, Abou-Karam M, Shier WT: Phytotoxic Responses of Soybean (Glycine max L.) to Botryodiplodin, a Toxin Produced by the Charcoal Rot Disease Fungus, Macrophomina phaseolina. Toxins (Basel). 2020 Jan 1;12(1). pii: toxins12010025. doi: 10.3390/toxins12010025. [PubMed:31906290 ]
Abbas HK, Bellaloui N, Accinelli C, Smith JR, Shier WT: Toxin Production in Soybean (Glycine max L.) Plants with Charcoal Rot Disease and by Macrophomina phaseolina, the Fungus that Causes the Disease. Toxins (Basel). 2019 Nov 6;11(11). pii: toxins11110645. doi: 10.3390/toxins11110645. [PubMed:31698804 ]
Felix C, Salvatore MM, DellaGreca M, Ferreira V, Duarte AS, Salvatore F, Naviglio D, Gallo M, Alves A, Esteves AC, Andolfi A: Secondary metabolites produced by grapevine strains of Lasiodiplodia theobromae grown at two different temperatures. Mycologia. 2019 May-Jun;111(3):466-476. doi: 10.1080/00275514.2019.1600342. Epub 2019 Apr 26. [PubMed:31025901 ]
Mioso R, Toledo Marante FJ, Herrera Bravo de Laguna I: Penicillium roqueforti: a multifunctional cell factory of high value-added molecules. J Appl Microbiol. 2015 Apr;118(4):781-91. doi: 10.1111/jam.12706. Epub 2014 Dec 29. [PubMed:25421646 ]
Ramezani M, Shier WT, Abbas HK, Tonos JL, Baird RE, Sciumbato GL: Soybean charcoal rot disease fungus Macrophomina phaseolina in Mississippi produces the phytotoxin (-)-botryodiplodin but no detectable phaseolinone. J Nat Prod. 2007 Jan;70(1):128-9. doi: 10.1021/np060480t. [PubMed:17253865 ]

Showing NP-Card for PSX 1 (NP0021496)

MOL for NP0021496 (PSX 1)

3D MOL for NP0021496 (PSX 1)

3D SDF for NP0021496 (PSX 1)

3D-SDF for NP0021496 (PSX 1)

PDB for NP0021496 (PSX 1)

3D PDB for NP0021496 (PSX 1)

SMILES for NP0021496 (PSX 1)

INCHI for NP0021496 (PSX 1)

Structure for NP0021496 (PSX 1)

3D Structure for NP0021496 (PSX 1)