MiMeDB: Showing metabocard for Rhizocticin A (MMDBc0017468)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2021-05-15 07:50:51 UTC

Update Date

2025-10-07 16:06:41 UTC

Metabolite ID

MMDBc0017468

Metabolite Identification

Common Name

Rhizocticin A

Description

Rhizocticin A is a lipopeptide belonging to the chemical class of secondary metabolites. It is synthesized by specific bacterial strains and is involved in various biosynthetic pathways that contribute to biocontrol activities against fungal pathogens. Genome mining studies have identified Rhizocticin A as part of several biosynthetic gene clusters, indicating its role alongside other metabolites such as bacilysin and surfactin in antagonistic interactions (PMID:39861562 ). Additionally, Rhizocticin A was exclusively detected in the genome of wild-type strains, highlighting its unique biosynthetic potential compared to mutant strains (PMID:39339553 ). The presence of Rhizocticin A in the biosynthetic repertoire of certain actinomycetes suggests its importance in the production of antifungal compounds (PMID:39770806 ). Furthermore, research has indicated that Rhizocticin A can be synthesized through stereoselective chemical processes, showcasing its potential as a target for synthetic biology and medicinal chemistry (PMID:23891162 ). Overall, Rhizocticin A exemplifies the intricate relationship between microbial metabolism and the development of biocontrol agents in agricultural applications.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652305152109502D          

 27 26  0  0  1  0            999 V2000
   -0.9355   -1.0164    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2224   -2.6664    0.0000 C   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
   -4.5079   -2.2539    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2211   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9368   -2.2539    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3645   -1.0164    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -4.5079   -1.4289    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.0789   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2224   -1.0164    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2079   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3645   -0.1914    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.9224   -1.0164    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.2079   -2.2539    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.4934   -1.0164    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7934   -1.0164    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0789   -2.2539    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2224   -0.1914    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9368   -1.4289    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.3658   -3.0789    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0638   -1.9520    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2388   -3.3809    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.6513   -2.6664    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2224   -3.4914    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7934   -2.6664    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3645   -1.8414    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2224   -1.8414    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  1  0  0  0  0
  4  2  2  0  0  0  0
  5  1  1  0  0  0  0
  6  2  1  0  0  0  0
  7  3  1  0  0  0  0
  8  4  1  0  0  0  0
  9  7  1  0  0  0  0
 10  8  1  0  0  0  0
  7 12  1  6  0  0  0
 13 11  2  0  0  0  0
 14 11  1  0  0  0  0
 15  5  1  0  0  0  0
 15 11  1  0  0  0  0
  8 16  1  6  0  0  0
 16  9  2  0  0  0  0
  9 17  1  4  0  0  0
 18 10  2  0  0  0  0
 19 10  1  0  0  0  0
 23  6  1  0  0  0  0
 23 20  1  0  0  0  0
 23 21  1  0  0  0  0
 23 22  2  0  0  0  0
 24  2  1  0  0  0  0
 25  4  1  0  0  0  0
  7 26  1  6  0  0  0
  8 27  1  6  0  0  0
M  END


  Mrv1652305152109502D          

 27 26  0  0  1  0            999 V2000
   -0.9355   -1.0164    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2224   -2.6664    0.0000 C   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
   -4.5079   -2.2539    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2211   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9368   -2.2539    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3645   -1.0164    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -4.5079   -1.4289    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.0789   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2224   -1.0164    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2079   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3645   -0.1914    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.9224   -1.0164    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.2079   -2.2539    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.4934   -1.0164    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7934   -1.0164    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0789   -2.2539    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2224   -0.1914    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9368   -1.4289    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.3658   -3.0789    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0638   -1.9520    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2388   -3.3809    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.6513   -2.6664    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2224   -3.4914    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7934   -2.6664    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3645   -1.8414    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2224   -1.8414    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  1  0  0  0  0
  4  2  2  0  0  0  0
  5  1  1  0  0  0  0
  6  2  1  0  0  0  0
  7  3  1  0  0  0  0
  8  4  1  0  0  0  0
  9  7  1  0  0  0  0
 10  8  1  0  0  0  0
  7 12  1  6  0  0  0
 13 11  2  0  0  0  0
 14 11  1  0  0  0  0
 15  5  1  0  0  0  0
 15 11  1  0  0  0  0
  8 16  1  6  0  0  0
 16  9  2  0  0  0  0
  9 17  1  4  0  0  0
 18 10  2  0  0  0  0
 19 10  1  0  0  0  0
 23  6  1  0  0  0  0
 23 20  1  0  0  0  0
 23 21  1  0  0  0  0
 23 22  2  0  0  0  0
 24  2  1  0  0  0  0
 25  4  1  0  0  0  0
  7 26  1  6  0  0  0
  8 27  1  6  0  0  0
M  END
> <DATABASE_ID>
MMDBc0017468

> <DATABASE_NAME>
MIME

> <SMILES>
[H]\C(CP(O)(O)=O)=C(/[H])[C@]([H])(N=C(O)[C@@]([H])(N)CCCNC(N)=N)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C11H22N5O6P/c12-7(3-1-5-15-11(13)14)9(17)16-8(10(18)19)4-2-6-23(20,21)22/h2,4,7-8H,1,3,5-6,12H2,(H,16,17)(H,18,19)(H4,13,14,15)(H2,20,21,22)/b4-2-/t7-,8-/m0/s1

> <INCHI_KEY>
BLNRPHBKOMCMBX-ABXVWLFBSA-N

> <FORMULA>
C11H22N5O6P

> <MOLECULAR_WEIGHT>
351.3

> <EXACT_MASS>
351.130770446

> <JCHEM_ACCEPTOR_COUNT>
11

> <JCHEM_ATOM_COUNT>
45

> <JCHEM_AVERAGE_POLARIZABILITY>
32.87738516312115

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
8

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S,3Z)-2-{[(2S)-2-amino-5-carbamimidamido-1-hydroxypentylidene]amino}-5-phosphonopent-3-enoic acid

> <ALOGPS_LOGP>
-2.68

> <JCHEM_LOGP>
-6.407208941971385

> <ALOGPS_LOGS>
-3.07

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
3.270708087539843

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.7312010708086736

> <JCHEM_PKA_STRONGEST_BASIC>
12.075409265190563

> <JCHEM_POLAR_SURFACE_AREA>
215.33999999999997

> <JCHEM_REFRACTIVITY>
92.64499999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
10

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
2.98e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2S,3Z)-2-{[(2S)-2-amino-5-carbamimidamido-1-hydroxypentylidene]amino}-5-phosphonopent-3-enoic 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      -1.746  -1.897   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -9.748  -4.977   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -3.080  -2.667   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -8.415  -4.207   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -0.413  -2.667   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0     -11.082  -4.207   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -4.414  -1.897   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -8.415  -2.667   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -5.747  -2.667   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -9.748  -1.897   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       2.255  -2.667   0.000  0.00  0.00           C+0
HETATM   12  N   UNK     0      -4.414  -0.357   0.000  0.00  0.00           N+0
HETATM   13  N   UNK     0       3.588  -1.897   0.000  0.00  0.00           N+0
HETATM   14  N   UNK     0       2.255  -4.207   0.000  0.00  0.00           N+0
HETATM   15  N   UNK     0       0.921  -1.897   0.000  0.00  0.00           N+0
HETATM   16  N   UNK     0      -7.081  -1.897   0.000  0.00  0.00           N+0
HETATM   17  O   UNK     0      -5.747  -4.207   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0      -9.748  -0.357   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0     -11.082  -2.667   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0     -13.749  -5.747   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0     -13.186  -3.644   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0     -11.646  -6.311   0.000  0.00  0.00           O+0
HETATM   23  P   UNK     0     -12.416  -4.977   0.000  0.00  0.00           P+0
HETATM   24  H   UNK     0      -9.748  -6.517   0.000  0.00  0.00           H+0
HETATM   25  H   UNK     0      -7.081  -4.977   0.000  0.00  0.00           H+0
HETATM   26  H   UNK     0      -4.414  -3.437   0.000  0.00  0.00           H+0
HETATM   27  H   UNK     0      -9.748  -3.437   0.000  0.00  0.00           H+0
CONECT    1    3    5                                                       
CONECT    2    4    6   24                                                  
CONECT    3    1    7                                                       
CONECT    4    2    8   25                                                  
CONECT    5    1   15                                                       
CONECT    6    2   23                                                       
CONECT    7    3    9   12   26                                             
CONECT    8    4   10   16   27                                             
CONECT    9    7   16   17                                                  
CONECT   10    8   18   19                                                  
CONECT   11   13   14   15                                                  
CONECT   12    7                                                            
CONECT   13   11                                                            
CONECT   14   11                                                            
CONECT   15    5   11                                                       
CONECT   16    8    9                                                       
CONECT   17    9                                                            
CONECT   18   10                                                            
CONECT   19   10                                                            
CONECT   20   23                                                            
CONECT   21   23                                                            
CONECT   22   23                                                            
CONECT   23    6   20   21   22                                             
CONECT   24    2                                                            
CONECT   25    4                                                            
CONECT   26    7                                                            
CONECT   27    8                                                            
MASTER        0    0    0    0    0    0    0    0   27    0   52    0
END

Synonyms

Value	Source
Arg-appa	MeSH
Arginyl-2-amino-5-phosphono-3-pentenoic acid	MeSH

Molecular Formula

C₁₁H₂₂N₅O₆P

Average Mass

351.3

Monoisotopic Mass

351.130770446

IUPAC Name

(2S,3Z)-2-{[(2S)-2-amino-5-carbamimidamido-1-hydroxypentylidene]amino}-5-phosphonopent-3-enoic acid

Traditional Name

(2S,3Z)-2-{[(2S)-2-amino-5-carbamimidamido-1-hydroxypentylidene]amino}-5-phosphonopent-3-enoic acid

CAS Registry Number

Not Available

SMILES

[H]\C(CP(O)(O)=O)=C(/[H])[C@]([H])(N=C(O)[C@@]([H])(N)CCCNC(N)=N)C(O)=O

InChI Identifier

InChI=1S/C11H22N5O6P/c12-7(3-1-5-15-11(13)14)9(17)16-8(10(18)19)4-2-6-23(20,21)22/h2,4,7-8H,1,3,5-6,12H2,(H,16,17)(H,18,19)(H4,13,14,15)(H2,20,21,22)/b4-2-/t7-,8-/m0/s1

InChI Key

BLNRPHBKOMCMBX-ABXVWLFBSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as dipeptides. These are organic compounds containing a sequence of exactly two alpha-amino acids joined by a peptide bond.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

Dipeptides

Alternative Parents

Substituents

Alpha-dipeptide
N-acyl-alpha-amino acid
N-acyl-alpha amino acid or derivatives
N-acyl-l-alpha-amino acid
Alpha-amino acid amide
Alpha-amino acid or derivatives
Fatty amide
N-acyl-amine
Fatty acyl
Fatty acid
Unsaturated fatty acid
Organophosphonic acid
Organophosphonic acid derivative
Amino acid or derivatives
Carboxamide group
Guanidine
Amino acid
Secondary carboxylic acid amide
Carboximidamide
Propargyl-type 1,3-dipolar organic compound
Organic 1,3-dipolar compound
Carboxylic acid
Monocarboxylic acid or derivatives
Organonitrogen compound
Organic oxide
Amine
Primary aliphatic amine
Organic oxygen compound
Organopnictogen compound
Hydrocarbon derivative
Organic nitrogen compound
Carbonyl group
Organooxygen compound
Organophosphorus compound
Primary amine
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

peptide (CHEBI:81400 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	0.3 g/L	ALOGPS
logP	-2.7	ALOGPS
logP	-6.4	ChemAxon
logS	-3.1	ALOGPS
pKa (Strongest Acidic)	1.73	ChemAxon
pKa (Strongest Basic)	12.08	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	11	ChemAxon
Hydrogen Donor Count	8	ChemAxon
Polar Surface Area	215.34 Å²	ChemAxon
Rotatable Bond Count	10	ChemAxon
Refractivity	92.64 m³·mol⁻¹	ChemAxon
Polarizability	32.88 Å³	ChemAxon
Number of Rings	0	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	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

This table shows at most 5 pathways. For the full list of associated pathways:

See All Associated Bacterial Pathways

Name	SMPDB/PathBank	Species

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	Firmicutes	1	Human	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

20145035

KEGG Compound ID

C17944

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

14061801

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

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 Rhizocticin A (MMDBc0017468)

MOL for #<Metabolite:0x00007f2ac5461af8>

3D MOL for #<Metabolite:0x00007f2ac5461af8>

3D SDF for #<Metabolite:0x00007f2ac5461af8>

3D-SDF for #<Metabolite:0x00007f2ac5461af8>

PDB for #<Metabolite:0x00007f2ac5461af8>

3D PDB for #<Metabolite:0x00007f2ac5461af8>

SMILES for #<Metabolite:0x00007f2ac5461af8>

INCHI for #<Metabolite:0x00007f2ac5461af8>

Structure for #<Metabolite:0x00007f2ac5461af8>

3D Structure for #<Metabolite:0x00007f2ac5461af8>