MiMeDB: Showing metabocard for Pantocin B (MMDBc0028713)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-05-15 18:27:42 UTC

Update Date

2022-08-31 06:53:53 UTC

Metabolite ID

MMDBc0028713

Metabolite Identification

Common Name

Pantocin B

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. Based on a literature review a small amount of articles have been published on Pantocin B.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652305152120272D          

 21 20  0  0  1  0            999 V2000
    2.0625    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4125   -5.0013    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -2.8579    0.0000 C   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
    1.2375    0.7145    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.4125   -3.5724    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
    0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2375   -3.5724    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    1.4289    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -1.4289    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 N   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
    1.2375   -0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6500   -4.2868    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6500   -2.8579    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -4.6993    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -3.8743    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -4.2868    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    1.6500    0.0000    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8250   -2.8579    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  5  1  1  0  0  0  0
  6  3  1  1  0  0  0
  7  3  1  0  0  0  0
  8  5  1  0  0  0  0
  9  6  1  0  0  0  0
  5 10  1  6  0  0  0
 11  4  1  4  0  0  0
 11  7  2  0  0  0  0
 12  4  1  4  0  0  0
 12  8  2  0  0  0  0
 13  7  1  0  0  0  0
 14  8  1  0  0  0  0
 15  9  2  0  0  0  0
 16  9  1  0  0  0  0
 19  2  1  0  0  0  0
 19  6  1  0  0  0  0
 19 17  2  0  0  0  0
 19 18  2  0  0  0  0
  5 20  1  6  0  0  0
  6 21  1  6  0  0  0
M  END
> <DATABASE_ID>
MMDBc0028713

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@@](C)(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                                 15-MAY-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   15-MAY-21         0                                  
HETATM    1  C   UNK     0       3.850   1.334   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.770  -9.336   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.000  -5.335   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -0.770  -1.334   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.310   1.334   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -0.770  -6.668   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -0.770  -4.001   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       1.540   0.000   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -2.310  -6.668   0.000  0.00  0.00           C+0
HETATM   10  N   UNK     0       1.540   2.667   0.000  0.00  0.00           N+0
HETATM   11  N   UNK     0       0.000  -2.667   0.000  0.00  0.00           N+0
HETATM   12  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   13  O   UNK     0      -2.310  -4.001   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0       2.310  -1.334   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0      -3.080  -8.002   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0      -3.080  -5.335   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0      -1.334  -8.772   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0       1.334  -7.232   0.000  0.00  0.00           O+0
HETATM   19  S   UNK     0       0.000  -8.002   0.000  0.00  0.00           S+0
HETATM   20  H   UNK     0       3.080   0.000   0.000  0.00  0.00           H+0
HETATM   21  H   UNK     0      -1.540  -5.335   0.000  0.00  0.00           H+0
CONECT    1    5                                                            
CONECT    2   19                                                            
CONECT    3    6    7                                                       
CONECT    4   11   12                                                       
CONECT    5    1    8   10   20                                             
CONECT    6    3    9   19   21                                             
CONECT    7    3   11   13                                                  
CONECT    8    5   12   14                                                  
CONECT    9    6   15   16                                                  
CONECT   10    5                                                            
CONECT   11    4    7                                                       
CONECT   12    4    8                                                       
CONECT   13    7                                                            
CONECT   14    8                                                            
CONECT   15    9                                                            
CONECT   16    9                                                            
CONECT   17   19                                                            
CONECT   18   19                                                            
CONECT   19    2    6   17   18                                             
CONECT   20    5                                                            
CONECT   21    6                                                            
MASTER        0    0    0    0    0    0    0    0   21    0   40    0
END

Synonyms

Value	Source
Pantocin-b	MeSH

Molecular Formula

C₉H₁₇N₃O₆S

Average Mass

295.31

Monoisotopic Mass

295.083806453

IUPAC Name

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

Traditional Name

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

CAS Registry Number

Not Available

SMILES

[H][C@@](C)(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

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

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	3.01 g/L	ALOGPS
logP	-2.9	ALOGPS
logP	-4.1	ChemAxon
logS	-2	ALOGPS
pKa (Strongest Acidic)	2.78	ChemAxon
pKa (Strongest Basic)	9.17	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	9	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	162.64 Å²	ChemAxon
Rotatable Bond Count	7	ChemAxon
Refractivity	64.72 m³·mol⁻¹	ChemAxon
Polarizability	27.55 Å³	ChemAxon
Number of Rings	0	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Not Available

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Protein ID	Protein Name	Protein Type	Uniprot ID	Species

Human Pathways

Pathways

Name	SMPDB/PathBank

Metabolic Reactions

Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Evidence Type	Host and Biospecimen	Data Source	Reference

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
Bacteria/Eubacteria	Proteobacteria	1	Human	Metabolic reconstruction

Exposure Sources

Source Type	Activity	Data Source	Reference

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB 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

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

van Santen JA, Poynton EF, Iskakova D, McMann E, Alsup TA, Clark TN, Fergusson CH, Fewer DP, Hughes AH, McCadden CA, Parra J, Soldatou S, Rudolf JD, Janssen EM, Duncan KR, Linington RG: The Natural Products Atlas 2.0: a database of microbially-derived natural products. Nucleic Acids Res. 2022 Jan 7;50(D1):D1317-D1323. doi: 10.1093/nar/gkab941. [PubMed:34718710 ]

Showing metabocard for Pantocin B (MMDBc0028713)

MOL for #<Metabolite:0x00007f3e140dc268>

3D MOL for #<Metabolite:0x00007f3e140dc268>

3D SDF for #<Metabolite:0x00007f3e140dc268>

3D-SDF for #<Metabolite:0x00007f3e140dc268>

PDB for #<Metabolite:0x00007f3e140dc268>

3D PDB for #<Metabolite:0x00007f3e140dc268>

SMILES for #<Metabolite:0x00007f3e140dc268>

INCHI for #<Metabolite:0x00007f3e140dc268>

Structure for #<Metabolite:0x00007f3e140dc268>

3D Structure for #<Metabolite:0x00007f3e140dc268>