NP-MRD: Showing NP-Card for Phosphonomycin (NP0021751)

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Record Information

Version

1.0

Created at

2021-01-06 07:01:24 UTC

Updated at

2021-07-15 17:37:11 UTC

NP-MRD ID

NP0021751

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Phosphonomycin

Provided By

NPAtlas

Description

Fosfomycin, also known as phosphonomycin or FCM, belongs to the class of organic compounds known as organic phosphonic acids. These are organic compounds containing phosphonic acid. Fosfomycin is a primary metabolite. Primary metabolites are metabolically or physiologically essential metabolites. They are directly involved in an organism’s growth, development or reproduction. Phosphonomycin is found in Pseudomonas syringae, Pseudomonas viridiflava and Streptomyces fradiae. It was first documented in 1969 (PMID: 5809587). Based on a literature review a significant number of articles have been published on Fosfomycin (PMID: 23438684) (PMID: 25599412) (PMID: 105327) (PMID: 17124631).

Structure

MOL 3D MOL SDF 3D SDF PDB SMILES InChI


  Mrv1652306242105183D          

 15 15  0  0  0  0            999 V2000
    1.8965    0.0839   -0.5846 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2871   -0.0232    0.8078 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.5768   -1.1761    1.1233 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1257    0.1268    0.9652 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.3173   -0.0438   -0.3635 P   0  0  2  0  0  5  0  0  0  0  0  0
   -0.6288   -0.6219   -1.5758 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0345    1.3984   -0.7779 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5399   -1.1042    0.1973 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0127    0.2402   -0.5238 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7502   -0.8558   -1.1568 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4714    0.9583   -1.1229 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9623    0.3096    1.6003 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5384    0.4324    1.9402 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0770    2.0625   -0.0550 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6954   -1.7873   -0.4739 H   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
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  5  7  1  6  0  0  0
  5  8  1  0  0  0  0
  4  2  1  0  0  0  0
  1  9  1  0  0  0  0
  1 10  1  0  0  0  0
  1 11  1  0  0  0  0
  2 12  1  1  0  0  0
  4 13  1  1  0  0  0
  7 14  1  0  0  0  0
  8 15  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0021751

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C3H7O4P/c1-2-3(7-2)8(4,5)6/h2-3H,1H3,(H2,4,5,6)/t2-,3+/m0/s1

> <INCHI_KEY>
YMDXZJFXQJVXBF-STHAYSLISA-N

> <FORMULA>
C3H7O4P

> <MOLECULAR_WEIGHT>
138.059

> <EXACT_MASS>
138.008195224

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
15

> <JCHEM_AVERAGE_POLARIZABILITY>
10.802823765292468

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
[(2R,3S)-3-methyloxiran-2-yl]phosphonic acid

> <ALOGPS_LOGP>
-0.86

> <JCHEM_LOGP>
-0.7377748799999998

> <ALOGPS_LOGS>
-0.47

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
7.82082800096408

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.2504967658604222

> <JCHEM_PKA_STRONGEST_BASIC>
-4.306369310142532

> <JCHEM_POLAR_SURFACE_AREA>
70.06

> <JCHEM_REFRACTIVITY>
25.8737

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.69e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
fosfomycin

> <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       1.897   0.084  -0.585  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.287  -0.023   0.808  0.00  0.00           C+0
HETATM    3  O   UNK     0       0.577  -1.176   1.123  0.00  0.00           O+0
HETATM    4  C   UNK     0      -0.126   0.127   0.965  0.00  0.00           C+0
HETATM    5  P   UNK     0      -1.317  -0.044  -0.364  0.00  0.00           P+0
HETATM    6  O   UNK     0      -0.629  -0.622  -1.576  0.00  0.00           O+0
HETATM    7  O   UNK     0      -2.034   1.398  -0.778  0.00  0.00           O+0
HETATM    8  O   UNK     0      -2.540  -1.104   0.197  0.00  0.00           O+0
HETATM    9  H   UNK     0       3.013   0.240  -0.524  0.00  0.00           H+0
HETATM   10  H   UNK     0       1.750  -0.856  -1.157  0.00  0.00           H+0
HETATM   11  H   UNK     0       1.471   0.958  -1.123  0.00  0.00           H+0
HETATM   12  H   UNK     0       1.962   0.310   1.600  0.00  0.00           H+0
HETATM   13  H   UNK     0      -0.538   0.432   1.940  0.00  0.00           H+0
HETATM   14  H   UNK     0      -2.077   2.063  -0.055  0.00  0.00           H+0
HETATM   15  H   UNK     0      -2.695  -1.787  -0.474  0.00  0.00           H+0
CONECT    1    2    9   10   11                                             
CONECT    2    1    3    4   12                                             
CONECT    3    2    4                                                       
CONECT    4    3    5    2   13                                             
CONECT    5    4    6    7    8                                             
CONECT    6    5                                                            
CONECT    7    5   14                                                       
CONECT    8    5   15                                                       
CONECT    9    1                                                            
CONECT   10    1                                                            
CONECT   11    1                                                            
CONECT   12    2                                                            
CONECT   13    4                                                            
CONECT   14    7                                                            
CONECT   15    8                                                            
MASTER        0    0    0    0    0    0    0    0   15    0   30    0
END

View in JSmol View NMR Assignments

Synonyms

Value	Source
(-)-(1R,2S)-(1,2-Epoxypropyl)phosphonic acid	ChEBI
(1R,2S)-Epoxypropylphosphonic acid	ChEBI
(2R-cis)-(3-Methyloxiranyl)phosphonic acid	ChEBI
1R-cis-(1,2-Epoxypropyl)phosphonic acid	ChEBI
cis-(1R,2S)-Epoxypropylphosphonic acid	ChEBI
FCM	ChEBI
Fosfomicina	ChEBI
Fosfomycine	ChEBI
Fosfomycinum	ChEBI
L-cis-1,2-Epoxypropylphosphonic acid	ChEBI
Phosphomycin	ChEBI
Phosphonemycin	ChEBI
Phosphonomycin	ChEBI
(1R,2S)-Epoxypropylphosphonate	Kegg
(-)-(1R,2S)-(1,2-Epoxypropyl)phosphonate	Generator
(2R-cis)-(3-Methyloxiranyl)phosphonate	Generator
1R-cis-(1,2-Epoxypropyl)phosphonate	Generator
cis-(1R,2S)-Epoxypropylphosphonate	Generator
L-cis-1,2-Epoxypropylphosphonate	Generator
Fosfomycin trometamol salt	MeSH
Monuril	MeSH
Tromethamine, fosfomycin	MeSH
Fosfomycin tromethamine	MeSH
Fosfocina	HMDB
Fosfomycin disodium salt	HMDB
Fosfomycin sodium	HMDB
Fosfonomycin	HMDB
Phosphomycin disodium salt	HMDB

Chemical Formula

C₃H₇O₄P

Average Mass

138.0590 Da

Monoisotopic Mass

138.00820 Da

IUPAC Name

[(2R,3S)-3-methyloxiran-2-yl]phosphonic acid

Traditional Name

fosfomycin

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C3H7O4P/c1-2-3(7-2)8(4,5)6/h2-3H,1H3,(H2,4,5,6)/t2-,3+/m0/s1

InChI Key

YMDXZJFXQJVXBF-STHAYSLISA-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
Pseudomonas syringae	LOTUS Database	35616633
Pseudomonas viridiflava	LOTUS Database	35616633
Streptomyces fradiae	NPAtlas	5809587

Species Where Detected

Species Name	Source	Reference
Streptomyces fradiae MA-2898 (NRRL B3357 ATCC 21096)	KNApSAcK Database	22123792
Streptomyces syringae	KNApSAcK Database	22123792
Streptomyces viridiflava	KNApSAcK Database	22123792
Streptomyces wedmorensis	KNApSAcK Database	22123792

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as organic phosphonic acids. These are organic compounds containing phosphonic acid.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Organic phosphonic acids and derivatives

Sub Class

Organic phosphonic acids

Direct Parent

Organic phosphonic acids

Alternative Parents

Not Available

Substituents

Not Available

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	-0.86	ALOGPS
logP	-0.74	ChemAxon
logS	-0.47	ALOGPS
pKa (Strongest Acidic)	1.25	ChemAxon
pKa (Strongest Basic)	-4.3	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	70.06 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	25.87 m³·mol⁻¹	ChemAxon
Polarizability	10.8 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

NPA024868

HMDB ID

HMDB0014966

DrugBank ID

DB00828

Phenol Explorer Compound ID

Not Available

FoodDB ID

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

BiGG ID

Not Available

Wikipedia Link

Fosfomycin

METLIN ID

Not Available

PubChem Compound

446987

PDB ID

Not Available

ChEBI ID

28915

Good Scents ID

Not Available

References

General References

Melzer N, Wittenburg D, Hartwig S, Jakubowski S, Kesting U, Willmitzer L, Lisec J, Reinsch N, Repsilber D: Investigating associations between milk metabolite profiles and milk traits of Holstein cows. J Dairy Sci. 2013 Mar;96(3):1521-34. doi: 10.3168/jds.2012-5743. [PubMed:23438684 ]
Hendlin D, Stapley EO, Jackson M, Wallick H, Miller AK, Wolf FJ, Miller TW, Chaiet L, Kahan FM, Foltz EL, Woodruff HB, Mata JM, Hernandez S, Mochales S: Phosphonomycin, a new antibiotic produced by strains of streptomyces. Science. 1969 Oct 3;166(3901):122-3. doi: 10.1126/science.166.3901.122. [PubMed:5809587 ]
Sun HZ, Wang DM, Wang B, Wang JK, Liu HY, Guan le L, Liu JX: Metabolomics of four biofluids from dairy cows: potential biomarkers for milk production and quality. J Proteome Res. 2015 Feb 6;14(2):1287-98. doi: 10.1021/pr501305g. Epub 2015 Jan 28. [PubMed:25599412 ]
Schena FP, Selvaggi FP, Montagna MT, Salvatore C: [Antibacterial activity of fosfomycin in chronic kidney infections]. Minerva Med. 1978 Dec 1;69(59):4097-104. [PubMed:105327 ]
Klein CD, Bachelier A: Molecular modeling and bioinformatical analysis of the antibacterial target enzyme MurA from a drug design perspective. J Comput Aided Mol Des. 2006 Oct-Nov;20(10-11):621-8. doi: 10.1007/s10822-006-9062-2. Epub 2006 Nov 24. [PubMed:17124631 ]

Showing NP-Card for Phosphonomycin (NP0021751)

MOL for NP0021751 (Phosphonomycin)

3D MOL for NP0021751 (Phosphonomycin)

3D SDF for NP0021751 (Phosphonomycin)

3D-SDF for NP0021751 (Phosphonomycin)

PDB for NP0021751 (Phosphonomycin)

3D PDB for NP0021751 (Phosphonomycin)

SMILES for NP0021751 (Phosphonomycin)

INCHI for NP0021751 (Phosphonomycin)

Structure for NP0021751 (Phosphonomycin)

3D Structure for NP0021751 (Phosphonomycin)