MiMeDB: Showing metabocard for Pyrrolnitrin (MMDBc0018838)

Pharmaceutical

Xenobiotic

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2021-05-15 08:59:36 UTC

Update Date

2025-10-07 16:06:53 UTC

Metabolite ID

MMDBc0018838

Metabolite Identification

Common Name

Pyrrolnitrin

Description

Pyrrolnitrin is a pyrrole derivative belonging to the class of antifungal metabolites. Its chemical structure is characterized as 3-chloro-4-[2'-nitro-3'-chlorophenyl]-pyrrole, which contributes to its biological activity. The biosynthesis of pyrrolnitrin involves a key enzyme, PrnB, which is classified within the heme-dependent aromatic oxygenase superfamily. This enzyme catalyzes the conversion of 7-chloro-l-tryptophan to monodechloroaminopyrrolnitrin, a crucial step in the production of this compound (PMID:40827054 ). Pyrrolnitrin is produced by various strains of Burkholderia, including Burkholderia contaminans, which has been shown to utilize this metabolite to inhibit postharvest decays in blueberries caused by Botrytis cinerea (PMID:40497431 ). Additionally, pyrrolnitrin exhibits persistence in moist nonsterile soil, maintaining its antifungal activity for up to 30 days (PMID:40934404 ). It is also involved in pathways related to chemotaxis and the biosynthesis of other compounds such as hydrogen cyanide and pyoverdine (PMID:41034730 ). Overall, pyrrolnitrin's unique chemical structure and biosynthetic pathways underscore its significance in microbial ecology and potential agricultural applications.

Structure

MOL SDF PDB SMILES InChI


  Mrv1533004241514382D          

 16 17  0  0  0  0            999 V2000
    1.3222   -0.0616    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    1.3222    0.7634    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
    0.6078    1.1759    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0367    1.1759    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0367    2.0009    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3222    2.4134    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    2.7512    2.4134    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4656    2.0009    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4656    1.1759    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7512    0.7634    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7512   -0.0616    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0837   -0.5465    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3387   -1.3312    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.1637   -1.3312    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4186   -0.5465    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2032   -0.2916    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  2  4  1  0  0  0  0
  4  5  2  0  0  0  0
  5  6  1  0  0  0  0
  5  7  1  0  0  0  0
  7  8  2  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
  4 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  2  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  2  0  0  0  0
 11 15  1  0  0  0  0
 15 16  1  0  0  0  0
M  CHG  2   1  -1   2   1
M  END
> <DATABASE_ID>
MMDBc0018838

> <DATABASE_NAME>
MIME

> <SMILES>
[O-][N+](=O)C1=C(Cl)C=CC=C1C1=CNC=C1Cl

> <INCHI_IDENTIFIER>
InChI=1S/C10H6Cl2N2O2/c11-8-3-1-2-6(10(8)14(15)16)7-4-13-5-9(7)12/h1-5,13H

> <INCHI_KEY>
QJBZDBLBQWFTPZ-UHFFFAOYSA-N

> <FORMULA>
C10H6Cl2N2O2

> <MOLECULAR_WEIGHT>
257.07

> <EXACT_MASS>
255.9806328

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
22

> <JCHEM_AVERAGE_POLARIZABILITY>
22.535194748895407

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
3-chloro-4-(3-chloro-2-nitrophenyl)-1H-pyrrole

> <ALOGPS_LOGP>
3.86

> <JCHEM_LOGP>
3.848428832666667

> <ALOGPS_LOGS>
-3.55

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
15.061515816511207

> <JCHEM_POLAR_SURFACE_AREA>
58.93

> <JCHEM_REFRACTIVITY>
61.883100000000006

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
7.24e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
pyrrolnitrin

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 24-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-APR-15         0                                  
HETATM    1  O   UNK     0       2.468  -0.115   0.000  0.00  0.00           O-1
HETATM    2  N   UNK     0       2.468   1.425   0.000  0.00  0.00           N+1
HETATM    3  O   UNK     0       1.134   2.195   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0       3.802   2.195   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       3.802   3.735   0.000  0.00  0.00           C+0
HETATM    6 Cl   UNK     0       2.468   4.505   0.000  0.00  0.00          Cl+0
HETATM    7  C   UNK     0       5.136   4.505   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       6.469   3.735   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       6.469   2.195   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       5.136   1.425   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       5.136  -0.115   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       3.890  -1.020   0.000  0.00  0.00           C+0
HETATM   13  N   UNK     0       4.366  -2.485   0.000  0.00  0.00           N+0
HETATM   14  C   UNK     0       5.906  -2.485   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       6.381  -1.020   0.000  0.00  0.00           C+0
HETATM   16 Cl   UNK     0       7.846  -0.544   0.000  0.00  0.00          Cl+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5   10                                                  
CONECT    5    4    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9    4   11                                                  
CONECT   11   10   12   15                                                  
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   11   16                                                  
CONECT   16   15                                                            
MASTER        0    0    0    0    0    0    0    0   16    0   34    0
END

Synonyms

Value	Source
3-Chloro-4-(2'-nitro-3'-chlorophenyl)pyrrole	ChEBI
3-Chloro-4-(3-chloro-2-nitrophenyl)pyrrole	ChEBI
NSC 107654	ChEBI
NSC-107654	ChEBI
Pirrolnitrina	ChEBI
Pyrrolnitrine	ChEBI
Pyrrolnitrinum	ChEBI

Molecular Formula

C₁₀H₆Cl₂N₂O₂

Average Mass

257.07

Monoisotopic Mass

255.9806328

IUPAC Name

3-chloro-4-(3-chloro-2-nitrophenyl)-1H-pyrrole

Traditional Name

pyrrolnitrin

CAS Registry Number

Not Available

SMILES

[O-][N+](=O)C1=C(Cl)C=CC=C1C1=CNC=C1Cl

InChI Identifier

InChI=1S/C10H6Cl2N2O2/c11-8-3-1-2-6(10(8)14(15)16)7-4-13-5-9(7)12/h1-5,13H

InChI Key

QJBZDBLBQWFTPZ-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as phenylpyrroles. These are polycyclic aromatic compounds containing a benzene ring linked to a pyrrole ring through a CC or CN bond.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Pyrroles

Sub Class

Substituted pyrroles

Direct Parent

Phenylpyrroles

Alternative Parents

Substituents

3-phenylpyrrole
Nitrobenzene
Nitroaromatic compound
Chlorobenzene
Halobenzene
Aryl chloride
Aryl halide
Monocyclic benzene moiety
Benzenoid
Heteroaromatic compound
Organic nitro compound
C-nitro compound
Propargyl-type 1,3-dipolar organic compound
Allyl-type 1,3-dipolar organic compound
Azacycle
Organic oxoazanium
Organic 1,3-dipolar compound
Organonitrogen compound
Organochloride
Organohalogen compound
Hydrocarbon derivative
Organic oxide
Organopnictogen compound
Organic oxygen compound
Organic nitrogen compound
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

C-nitro compound (CHEBI:32079 )
indole alkaloid (CHEBI:32079 )
monochlorobenzenes (CHEBI:32079 )
ring assembly (CHEBI:32079 )
pyrroles (CHEBI:32079 )
a chloroaromatic compound (CPD-12776 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	0.072 g/L	ALOGPS
logP	3.86	ALOGPS
logP	3.85	ChemAxon
logS	-3.6	ALOGPS
pKa (Strongest Acidic)	15.06	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	2	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	58.93 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	61.88 m³·mol⁻¹	ChemAxon
Polarizability	22.54 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Spectrum Type	Description	Splash Key	Deposition Date	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0a4i-0090000000-f6ad5cd4ead742601b39	2016-08-01	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0udi-0090000000-9c7ee7a00096ebc769ad	2016-08-01	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0znc-0290000000-f8128d718262b7d8e34e	2016-08-01	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0udi-0090000000-be486096da708c149e42	2016-08-03	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0udi-0090000000-30c7238a5418140123e7	2016-08-03	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0uyu-2790000000-8e241ce25ed4df3902a2	2016-08-03	View Spectrum

Chromatographic Retention Times and Retention Indices

Retention Times

Chromatography Type	Technique	Column	Deposition Date	Retention Time (s)
Liquid Chromatography	HILIC	Waters Acquity UPLC-BEH Amide column (void)	2025-10-23	529.5
Liquid Chromatography	HILIC	Accucore 150 Amide HILIC (void)	2025-10-23	31.5
Liquid Chromatography	Reversed-phase	Hypersil Gold 1.9 µm C18 (eluted)	2025-10-23	444.1
Liquid Chromatography	Reversed-phase	Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) (eluted)	2025-10-23	575.4
Liquid Chromatography	Reversed-phase	XBridge C18 3.5u 2.1x50 mm (eluted)	2025-10-23	519.5
Liquid Chromatography	Reversed-phase	Ascentis Express C18 (void)	2025-10-23	542.9
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-23	1769.9
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-23	368.8
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC (eluted)	2025-10-23	637.1
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-23	453.9
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-23	496.7
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-23	348.7
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-23	196.5
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-23	39.2
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-23	539.5
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-23	324.3
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-23	399.6
Liquid Chromatography	Reversed-phase	Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex (eluted)	2025-10-23	1196.8
Liquid Chromatography	Reversed-phase	Waters Atlantis T3 (2.1 x 150 mm, 5 um) (eluted)	2025-10-23	1312.8

Retention Indices

Chromatography Type	Peak Label	SMILES	Stationary Phase	Deposition Date	Retention Index
Gas Chromatography	Pyrrolnitrin_TMS_1	C[Si](C)(C)N1C=C(Cl)C(C2=CC=CC(Cl)=C2[N+](=O)[O-])=C1	standard non polar	2025-10-23	1813.45
Gas Chromatography	Pyrrolnitrin_TMS_1	C[Si](C)(C)N1C=C(Cl)C(C2=CC=CC(Cl)=C2[N+](=O)[O-])=C1	standard polar	2025-10-23	1890.98

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	Human ; Human subgingival plaque; Human feces	Metabolic reconstruction
Bacteria	Proteobacteria	1	Human ; Human subgingival plaque; Human feces	Metabolic reconstruction

Exposure Sources

Other Exposures

Source Type	Data Source	Reference
Drugs - Antimicrobial	U.S. Environmental Protection Agency	CompTox
Cosmetics	U.S. Environmental Protection Agency	CompTox
Domestics	U.S. Environmental Protection Agency	CompTox

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

DB13603

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

C00018726

Chemspider ID

Not Available

KEGG Compound ID

C12491

BioCyc ID

CPD-12776

BiGG ID

Not Available

Wikipedia Link

Pyrrolnitrin

METLIN ID

Not Available

PubChem Compound

13916

PDB ID

Not Available

ChEBI ID

32079

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

Not Available

General References

Bansal P, Morgat A, Axelsen KB, Muthukrishnan V, Coudert E, Aimo L, Hyka-Nouspikel N, Gasteiger E, Kerhornou A, Neto TB, Pozzato M, Blatter MC, Ignatchenko A, Redaschi N, Bridge A: Rhea, the reaction knowledgebase in 2022. Nucleic Acids Res. 2022 Jan 7;50(D1):D693-D700. doi: 10.1093/nar/gkab1016. [PubMed:34755880 ]

Showing metabocard for Pyrrolnitrin (MMDBc0018838)

MOL for #<Metabolite:0x00007f9abeeb9118>

3D MOL for #<Metabolite:0x00007f9abeeb9118>

3D SDF for #<Metabolite:0x00007f9abeeb9118>

3D-SDF for #<Metabolite:0x00007f9abeeb9118>

PDB for #<Metabolite:0x00007f9abeeb9118>

3D PDB for #<Metabolite:0x00007f9abeeb9118>

SMILES for #<Metabolite:0x00007f9abeeb9118>

INCHI for #<Metabolite:0x00007f9abeeb9118>

Structure for #<Metabolite:0x00007f9abeeb9118>

3D Structure for #<Metabolite:0x00007f9abeeb9118>