NP-MRD: Showing NP-Card for (2r)-3-[({[(2s)-2-amino-1-hydroxypropylidene]amino}methyl)-c-hydroxycarbonimidoyl]-2-methanesulfonylpropanoic acid (NP0147471)

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Record Information

Version

2.0

Created at

2022-09-02 03:05:07 UTC

Updated at

2022-09-02 03:05:07 UTC

NP-MRD ID

NP0147471

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(2r)-3-[({[(2s)-2-amino-1-hydroxypropylidene]amino}methyl)-c-hydroxycarbonimidoyl]-2-methanesulfonylpropanoic acid

Description

Pantocin B, also known as pantocin-b, belongs to the class of organic compounds known as alpha amino acid amides. These are amide derivatives of alpha amino acids. (2r)-3-[({[(2s)-2-amino-1-hydroxypropylidene]amino}methyl)-c-hydroxycarbonimidoyl]-2-methanesulfonylpropanoic acid is found in Pantoea agglomerans. (2r)-3-[({[(2s)-2-amino-1-hydroxypropylidene]amino}methyl)-c-hydroxycarbonimidoyl]-2-methanesulfonylpropanoic acid was first documented in 2000 (PMID: 10814312). Based on a literature review a small amount of articles have been published on Pantocin B (PMID: 11592872) (PMID: 11133457).

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 36 35  0  0  0  0  0  0  0  0999 V2000
   -5.2448   -0.7084   -0.4217 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1419    0.1186    0.2025 C   0  0  2  0  0  0  0  0  0  0  0  0
   -4.6802    0.9893    1.2327 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4692    0.9942   -0.7910 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1603    1.9613   -1.5016 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2068    0.8700   -1.0162 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3994   -0.1169   -0.3187 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0479   -0.0645   -0.8088 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.8124   -0.9318   -0.4214 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4131   -1.9101    0.4709 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2186   -0.8924   -0.9197 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1052   -0.7205    0.2895 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.7334    0.5507    0.9609 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3220    0.6071    2.1455 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8354    1.7545    0.2688 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.8223   -0.7045   -0.1278 S   0  0  0  0  0  6  0  0  0  0  0  0
    5.2580    0.6010   -1.2098 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6038   -0.5953    1.1513 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.2083   -2.0038   -0.7681 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9748   -0.9983   -1.4770 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4300   -1.6370    0.1448 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2072   -0.1537   -0.4883 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4026   -0.5364    0.7003 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3381    0.5237    1.8680 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9522    1.9190    0.8925 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9033    2.9432   -1.3393 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4708    0.1203    0.7617 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8322   -1.1263   -0.4607 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5939   -2.8860    0.3772 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4622   -1.7792   -1.5113 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3774   -0.0038   -1.5621 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9177   -1.5702    0.9711 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0211    2.6443    0.7184 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.9946    0.2545   -1.9910 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3843    1.0959   -1.6844 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.7781    1.3915   -0.6300 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  4  6  2  0
  6  7  1  0
  7  8  1  0
  8  9  2  0
  9 10  1  0
  9 11  1  0
 11 12  1  0
 12 13  1  0
 13 15  1  0
 13 14  2  0
 12 16  1  0
 16 17  1  0
 16 18  2  0
 16 19  2  0
  1 20  1  0
  1 21  1  0
  1 22  1  0
  2 23  1  1
  3 24  1  0
  3 25  1  0
  5 26  1  0
  7 27  1  0
  7 28  1  0
 10 29  1  0
 11 30  1  0
 11 31  1  0
 12 32  1  1
 15 33  1  0
 17 34  1  0
 17 35  1  0
 17 36  1  0
M  END


  Mrv1652309022205052D          

 19 18  0  0  1  0            999 V2000
    3.7125   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3000    0.0000    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.7125    0.7145    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0625   -0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0625    0.7145    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125    0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -1.4289    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.4125   -2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2375   -2.1434    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -2.8579    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250   -1.4289    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    1.6500   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250   -2.2539    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250   -0.6039    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  1  0  0  0
  2  4  1  0  0  0  0
  4  5  1  0  0  0  0
  4  6  2  0  0  0  0
  6  7  1  4  0  0  0
  8  7  1  4  0  0  0
  8  9  2  0  0  0  0
  9 10  1  0  0  0  0
  9 11  1  0  0  0  0
 12 11  1  1  0  0  0
 12 13  1  0  0  0  0
 13 14  2  0  0  0  0
 13 15  1  0  0  0  0
 12 16  1  0  0  0  0
 16 17  1  0  0  0  0
 16 18  2  0  0  0  0
 16 19  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0147471

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@H](N)C(O)=NCN=C(O)C[C@H](C(O)=O)S(C)(=O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C9H17N3O6S/c1-5(10)8(14)12-4-11-7(13)3-6(9(15)16)19(2,17)18/h5-6H,3-4,10H2,1-2H3,(H,11,13)(H,12,14)(H,15,16)/t5-,6+/m0/s1

> <INCHI_KEY>
QPOFRFGIYSXYSK-NTSWFWBYSA-N

> <FORMULA>
C9H17N3O6S

> <MOLECULAR_WEIGHT>
295.31

> <EXACT_MASS>
295.083806453

> <JCHEM_ACCEPTOR_COUNT>
9

> <JCHEM_ATOM_COUNT>
36

> <JCHEM_AVERAGE_POLARIZABILITY>
27.54635341790514

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R)-3-[({[(2S)-2-amino-1-hydroxypropylidene]amino}methyl)-C-hydroxycarbonimidoyl]-2-methanesulfonylpropanoic acid

> <ALOGPS_LOGP>
-2.90

> <JCHEM_LOGP>
-4.119289684665772

> <ALOGPS_LOGS>
-1.99

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
3.4636960256444564

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.781869898205783

> <JCHEM_PKA_STRONGEST_BASIC>
9.168848786877204

> <JCHEM_POLAR_SURFACE_AREA>
162.64

> <JCHEM_REFRACTIVITY>
64.71690000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.01e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2R)-3-[({[(2S)-2-amino-1-hydroxypropylidene]amino}methyl)-C-hydroxycarbonimidoyl]-2-methanesulfonylpropanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 02-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   02-SEP-22         0                                  
HETATM    1  C   UNK     0       6.930  -1.334   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       6.160   0.000   0.000  0.00  0.00           C+0
HETATM    3  N   UNK     0       6.930   1.334   0.000  0.00  0.00           N+0
HETATM    4  C   UNK     0       4.620   0.000   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       3.850  -1.334   0.000  0.00  0.00           O+0
HETATM    6  N   UNK     0       3.850   1.334   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0       2.310   1.334   0.000  0.00  0.00           C+0
HETATM    8  N   UNK     0       1.540   0.000   0.000  0.00  0.00           N+0
HETATM    9  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      -0.770   1.334   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0      -0.770  -1.334   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       0.000  -2.667   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -0.770  -4.001   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0      -2.310  -4.001   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0       0.000  -5.335   0.000  0.00  0.00           O+0
HETATM   16  S   UNK     0       1.540  -2.667   0.000  0.00  0.00           S+0
HETATM   17  C   UNK     0       3.080  -2.667   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       1.540  -4.207   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0       1.540  -1.127   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9   12                                                       
CONECT   12   11   13   16                                                  
CONECT   13   12   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13                                                            
CONECT   16   12   17   18   19                                             
CONECT   17   16                                                            
CONECT   18   16                                                            
CONECT   19   16                                                            
MASTER        0    0    0    0    0    0    0    0   19    0   36    0
END

View in JSmol

Synonyms

Value	Source
Pantocin-b	MeSH

Chemical Formula

C₉H₁₇N₃O₆S

Average Mass

295.3100 Da

Monoisotopic Mass

295.08381 Da

IUPAC Name

Not Available

Traditional Name

Not Available

CAS Registry Number

Not Available

SMILES

C[C@H](N)C(O)=NCN=C(O)C[C@H](C(O)=O)S(C)(=O)=O

InChI Identifier

InChI=1S/C9H17N3O6S/c1-5(10)8(14)12-4-11-7(13)3-6(9(15)16)19(2,17)18/h5-6H,3-4,10H2,1-2H3,(H,11,13)(H,12,14)(H,15,16)/t5-,6+/m0/s1

InChI Key

QPOFRFGIYSXYSK-NTSWFWBYSA-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
Pantoea agglomerans	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as alpha amino acid amides. These are amide derivatives of alpha amino acids.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

Alpha amino acid amides

Alternative Parents

Substituents

Alpha-amino acid amide
Alanine or derivatives
Thia fatty acid
Fatty amide
N-acyl-amine
Fatty acid
Fatty acyl
Sulfonyl
Sulfone
Amino acid
Carboxamide group
Secondary carboxylic acid amide
Carboxylic acid
Monocarboxylic acid or derivatives
Organic oxide
Organooxygen compound
Organonitrogen compound
Organic nitrogen compound
Organosulfur compound
Primary aliphatic amine
Primary amine
Organic oxygen compound
Carbonyl group
Hydrocarbon derivative
Amine
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic 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

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

8812976

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

10637614

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Sutton AE, Clardy J: Synthesis and biological evaluation of analogues of the antibiotic pantocin B. J Am Chem Soc. 2001 Oct 17;123(41):9935-46. doi: 10.1021/ja003770j. [PubMed:11592872 ]
Wright SA, Zumoff CH, Schneider L, Beer SV: Pantoea agglomerans strain EH318 produces two antibiotics that inhibit Erwinia amylovora in vitro. Appl Environ Microbiol. 2001 Jan;67(1):284-92. doi: 10.1128/AEM.67.1.284-292.2001. [PubMed:11133457 ]
Sutton AE, Clardy J: The total synthesis of pantocin B. Org Lett. 2000 Feb 10;2(3):319-21. doi: 10.1021/ol991264x. [PubMed:10814312 ]
LOTUS database [Link]

Showing NP-Card for (2r)-3-[({[(2s)-2-amino-1-hydroxypropylidene]amino}methyl)-c-hydroxycarbonimidoyl]-2-methanesulfonylpropanoic acid (NP0147471)

MOL for NP0147471 ((2r)-3-[({[(2s)-2-amino-1-hydroxypropylidene]amino}methyl)-c-hydroxycarbonimidoyl]-2-methanesulfonylpropanoic acid)

3D MOL for NP0147471 ((2r)-3-[({[(2s)-2-amino-1-hydroxypropylidene]amino}methyl)-c-hydroxycarbonimidoyl]-2-methanesulfonylpropanoic acid)

3D SDF for NP0147471 ((2r)-3-[({[(2s)-2-amino-1-hydroxypropylidene]amino}methyl)-c-hydroxycarbonimidoyl]-2-methanesulfonylpropanoic acid)

3D-SDF for NP0147471 ((2r)-3-[({[(2s)-2-amino-1-hydroxypropylidene]amino}methyl)-c-hydroxycarbonimidoyl]-2-methanesulfonylpropanoic acid)

PDB for NP0147471 ((2r)-3-[({[(2s)-2-amino-1-hydroxypropylidene]amino}methyl)-c-hydroxycarbonimidoyl]-2-methanesulfonylpropanoic acid)

3D PDB for NP0147471 ((2r)-3-[({[(2s)-2-amino-1-hydroxypropylidene]amino}methyl)-c-hydroxycarbonimidoyl]-2-methanesulfonylpropanoic acid)

SMILES for NP0147471 ((2r)-3-[({[(2s)-2-amino-1-hydroxypropylidene]amino}methyl)-c-hydroxycarbonimidoyl]-2-methanesulfonylpropanoic acid)

INCHI for NP0147471 ((2r)-3-[({[(2s)-2-amino-1-hydroxypropylidene]amino}methyl)-c-hydroxycarbonimidoyl]-2-methanesulfonylpropanoic acid)

Structure for NP0147471 ((2r)-3-[({[(2s)-2-amino-1-hydroxypropylidene]amino}methyl)-c-hydroxycarbonimidoyl]-2-methanesulfonylpropanoic acid)

3D Structure for NP0147471 ((2r)-3-[({[(2s)-2-amino-1-hydroxypropylidene]amino}methyl)-c-hydroxycarbonimidoyl]-2-methanesulfonylpropanoic acid)