MiMeDB: Showing metabocard for Pantocin A (MMDBc0015409)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2021-05-15 06:13:53 UTC

Update Date

2025-10-07 16:06:24 UTC

Metabolite ID

MMDBc0015409

Metabolite Identification

Common Name

Pantocin A

Description

Pantocin A is a peptide-derived antibiotic belonging to the class of ribosomally synthesized and post-translationally modified peptides (RiPPs). This metabolite is produced by Pantoea species and plays a significant role in biological control, particularly against plant pathogens such as Erwinia amylovora. The biosynthesis of Pantocin A involves the enzyme PaaA, which catalyzes the transformation of glutamic acid residues into its bicyclic core structure (PMID:32109054 ). Studies indicate that Pantocin A exhibits a broad spectrum of antimicrobial activity, with its production linked to other metabolites like PNP-3, suggesting a complex interplay in the inhibition of various pathogens (PMID:32062363 ). Notably, the presence of Pantocin A has been confirmed through LC-MS/MS profiling, highlighting its significance among other bioactive compounds produced by different bacterial genera (PMID:40614942 ). Furthermore, research has demonstrated that mutants deficient in PNP-2 can still inhibit Erwinia amylovora, underscoring the importance of Pantocin A as a secondary antibiotic (PMID:32416447 ). Overall, Pantocin A represents a critical component of the antimicrobial arsenal of Pantoea, contributing to its ecological role in plant health.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652305152108132D          

 26 27  0  0  1  0            999 V2000
    0.1318    5.7411    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0876    4.8551    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9388    5.5696    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3426    4.0705    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1685    3.5116    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2807    5.0267    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0250    4.7491    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7905    3.4574    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.4540    3.0991    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.8829    3.0991    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2714    4.4136    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0164    3.6290    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7395    4.3366    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4540    2.2741    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0455    2.6728    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.5974    3.5116    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.7395    3.5116    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.8829    2.2741    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5685    3.0159    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4540    4.7491    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1685    1.8616    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7395    1.8616    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7169    5.1985    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5975    3.2859    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1685    2.6866    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8845    3.8615    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  2  0  0  0  0
  4  2  1  0  0  0  0
  6  1  1  0  0  0  0
  6  2  2  0  0  0  0
  7  3  1  0  0  0  0
  8  4  1  0  0  0  0
  9  5  1  0  0  0  0
 10  5  1  0  0  0  0
 11  6  1  0  0  0  0
 11  7  1  0  0  0  0
 12  8  1  0  0  0  0
 12 11  1  0  0  0  0
 13  7  1  0  0  0  0
 14  9  1  0  0  0  0
  8 15  1  1  0  0  0
 16 10  2  0  0  0  0
  9 17  1  6  0  0  0
 17 13  2  0  0  0  0
 18 10  1  0  0  0  0
 19 12  2  0  0  0  0
 13 20  1  4  0  0  0
 21 14  2  0  0  0  0
 22 14  1  0  0  0  0
 23  7  1  0  0  0  0
  8 24  1  6  0  0  0
  9 25  1  6  0  0  0
 26 11  1  0  0  0  0
M  END


  Mrv1652305152108132D          

 26 27  0  0  1  0            999 V2000
    0.1318    5.7411    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0876    4.8551    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9388    5.5696    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3426    4.0705    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1685    3.5116    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2807    5.0267    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0250    4.7491    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7905    3.4574    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.4540    3.0991    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.8829    3.0991    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2714    4.4136    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0164    3.6290    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7395    4.3366    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4540    2.2741    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0455    2.6728    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.5974    3.5116    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.7395    3.5116    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.8829    2.2741    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5685    3.0159    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4540    4.7491    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1685    1.8616    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7395    1.8616    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7169    5.1985    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5975    3.2859    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1685    2.6866    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8845    3.8615    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  2  0  0  0  0
  4  2  1  0  0  0  0
  6  1  1  0  0  0  0
  6  2  2  0  0  0  0
  7  3  1  0  0  0  0
  8  4  1  0  0  0  0
  9  5  1  0  0  0  0
 10  5  1  0  0  0  0
 11  6  1  0  0  0  0
 11  7  1  0  0  0  0
 12  8  1  0  0  0  0
 12 11  1  0  0  0  0
 13  7  1  0  0  0  0
 14  9  1  0  0  0  0
  8 15  1  1  0  0  0
 16 10  2  0  0  0  0
  9 17  1  6  0  0  0
 17 13  2  0  0  0  0
 18 10  1  0  0  0  0
 19 12  2  0  0  0  0
 13 20  1  4  0  0  0
 21 14  2  0  0  0  0
 22 14  1  0  0  0  0
 23  7  1  0  0  0  0
  8 24  1  6  0  0  0
  9 25  1  6  0  0  0
 26 11  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0015409

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@@](CC(O)=N)(N=C(O)C1([H])C=CC2=CC[C@]([H])(N)C(=O)C12[H])C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C14H17N3O5/c15-8-4-2-6-1-3-7(11(6)12(8)19)13(20)17-9(14(21)22)5-10(16)18/h1-3,7-9,11H,4-5,15H2,(H2,16,18)(H,17,20)(H,21,22)/t7?,8-,9-,11?/m0/s1

> <INCHI_KEY>
SOPAHPGXYDUTGN-QMFGVRBNSA-N

> <FORMULA>
C14H17N3O5

> <MOLECULAR_WEIGHT>
307.306

> <EXACT_MASS>
307.116820659

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_ATOM_COUNT>
39

> <JCHEM_AVERAGE_POLARIZABILITY>
29.357052790055764

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S)-2-({[(6S)-6-amino-7-oxo-5,6,7,7a-tetrahydro-1H-inden-1-yl](hydroxy)methylidene}amino)-3-(C-hydroxycarbonimidoyl)propanoic acid

> <ALOGPS_LOGP>
-2.12

> <JCHEM_LOGP>
-5.617952956417862

> <ALOGPS_LOGS>
-3.11

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
3.594123534050588

> <JCHEM_PKA_STRONGEST_ACIDIC>
-1.681223453346644

> <JCHEM_PKA_STRONGEST_BASIC>
12.589847282818818

> <JCHEM_POLAR_SURFACE_AREA>
157.06

> <JCHEM_REFRACTIVITY>
88.1388

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.36e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2S)-2-({[(6S)-6-amino-7-oxo-1,5,6,7a-tetrahydroinden-1-yl](hydroxy)methylidene}amino)-3-(C-hydroxycarbonimidoyl)propanoic 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       0.246  10.717   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -2.030   9.063   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.752  10.397   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -2.506   7.598   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       5.914   6.555   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -0.524   9.383   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       1.913   8.865   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -1.476   6.454   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       4.581   5.785   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       7.248   5.785   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       0.507   8.239   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       0.031   6.774   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       3.247   8.095   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       4.581   4.245   0.000  0.00  0.00           C+0
HETATM   15  N   UNK     0      -1.952   4.989   0.000  0.00  0.00           N+0
HETATM   16  N   UNK     0       8.582   6.555   0.000  0.00  0.00           N+0
HETATM   17  N   UNK     0       3.247   6.555   0.000  0.00  0.00           N+0
HETATM   18  O   UNK     0       7.248   4.245   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0       1.061   5.630   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0       4.581   8.865   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0       5.914   3.475   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0       3.247   3.475   0.000  0.00  0.00           O+0
HETATM   23  H   UNK     0       3.205   9.704   0.000  0.00  0.00           H+0
HETATM   24  H   UNK     0      -2.982   6.134   0.000  0.00  0.00           H+0
HETATM   25  H   UNK     0       5.914   5.015   0.000  0.00  0.00           H+0
HETATM   26  H   UNK     0       1.651   7.208   0.000  0.00  0.00           H+0
CONECT    1    3    6                                                       
CONECT    2    4    6                                                       
CONECT    3    1    7                                                       
CONECT    4    2    8                                                       
CONECT    5    9   10                                                       
CONECT    6    1    2   11                                                  
CONECT    7    3   11   13   23                                             
CONECT    8    4   12   15   24                                             
CONECT    9    5   14   17   25                                             
CONECT   10    5   16   18                                                  
CONECT   11    6    7   12   26                                             
CONECT   12    8   11   19                                                  
CONECT   13    7   17   20                                                  
CONECT   14    9   21   22                                                  
CONECT   15    8                                                            
CONECT   16   10                                                            
CONECT   17    9   13                                                       
CONECT   18   10                                                            
CONECT   19   12                                                            
CONECT   20   13                                                            
CONECT   21   14                                                            
CONECT   22   14                                                            
CONECT   23    7                                                            
CONECT   24    8                                                            
CONECT   25    9                                                            
CONECT   26   11                                                            
MASTER        0    0    0    0    0    0    0    0   26    0   54    0
END

Synonyms

Value	Source
(2S)-2-({[(6S)-6-amino-7-oxo-5,6,7,7a-tetrahydro-1H-inden-1-yl](hydroxy)methylidene}amino)-3-(C-hydroxycarbonimidoyl)propanoate	Generator

Molecular Formula

C₁₄H₁₇N₃O₅

Average Mass

307.306

Monoisotopic Mass

307.116820659

IUPAC Name

(2S)-2-({[(6S)-6-amino-7-oxo-5,6,7,7a-tetrahydro-1H-inden-1-yl](hydroxy)methylidene}amino)-3-(C-hydroxycarbonimidoyl)propanoic acid

Traditional Name

(2S)-2-({[(6S)-6-amino-7-oxo-1,5,6,7a-tetrahydroinden-1-yl](hydroxy)methylidene}amino)-3-(C-hydroxycarbonimidoyl)propanoic acid

CAS Registry Number

Not Available

SMILES

[H][C@@](CC(O)=N)(N=C(O)C1([H])C=CC2=CC[C@]([H])(N)C(=O)C12[H])C(O)=O

InChI Identifier

InChI=1S/C14H17N3O5/c15-8-4-2-6-1-3-7(11(6)12(8)19)13(20)17-9(14(21)22)5-10(16)18/h1-3,7-9,11H,4-5,15H2,(H2,16,18)(H,17,20)(H,21,22)/t7?,8-,9-,11?/m0/s1

InChI Key

SOPAHPGXYDUTGN-QMFGVRBNSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as asparagine and derivatives. Asparagine and derivatives are compounds containing asparagine or a derivative thereof resulting from reaction of asparagine at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

Asparagine and derivatives

Alternative Parents

Substituents

Asparagine or derivatives
Delta amino acid or derivatives
N-acyl-l-alpha-amino acid
N-acyl-alpha-amino acid
N-acyl-alpha amino acid or derivatives
Cyclohexenone
Fatty amide
Fatty acyl
Carboxamide group
Amino acid
Ketone
Secondary carboxylic acid amide
Primary carboxylic acid amide
Carboxylic acid
Monocarboxylic acid or derivatives
Amine
Organonitrogen compound
Organooxygen compound
Primary amine
Primary aliphatic amine
Hydrocarbon derivative
Organic oxide
Organopnictogen compound
Organic oxygen compound
Organic nitrogen compound
Carbonyl group
Aliphatic homopolycyclic compound

Molecular Framework

Aliphatic homopolycyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	0.24 g/L	ALOGPS
logP	-2.1	ALOGPS
logP	-5.6	ChemAxon
logS	-3.1	ALOGPS
pKa (Strongest Acidic)	-1.7	ChemAxon
pKa (Strongest Basic)	12.59	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	8	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	157.06 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	88.14 m³·mol⁻¹	ChemAxon
Polarizability	29.36 Å³	ChemAxon
Number of Rings	2	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

Microbial Pathways

Pathways

Not Available

Metabolic Reactions

Reactions

This table shows at most 20 reactions. For the full list of associated reactions:

See All Associated 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		Metabolic reconstruction

Exposure Sources

Other Exposures

Source Type	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

78438095

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

139587328

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

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 A (MMDBc0015409)

MOL for #<Metabolite:0x00007f8dc7f21280>

3D MOL for #<Metabolite:0x00007f8dc7f21280>

3D SDF for #<Metabolite:0x00007f8dc7f21280>

3D-SDF for #<Metabolite:0x00007f8dc7f21280>

PDB for #<Metabolite:0x00007f8dc7f21280>

3D PDB for #<Metabolite:0x00007f8dc7f21280>

SMILES for #<Metabolite:0x00007f8dc7f21280>

INCHI for #<Metabolite:0x00007f8dc7f21280>

Structure for #<Metabolite:0x00007f8dc7f21280>

3D Structure for #<Metabolite:0x00007f8dc7f21280>