MiMeDB: Showing metabocard for Isopenicillin N (MMDBc0053378)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2022-05-16 21:22:38 UTC

Update Date

2024-10-13 10:28:05 UTC

Metabolite ID

MMDBc0053378

Metabolite Identification

Common Name

Isopenicillin N

Description

Structure

MOL SDF PDB SMILES InChI


  Mrv0541 05041405552D          

 28 29  0  0  1  0            999 V2000
   11.1332    7.7127    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.0668    7.9984    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.6429    5.3469    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9284    4.9344    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.3573    4.9344    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2139    5.3469    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    8.0718    5.3469    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.5008    5.3469    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   10.9605    6.6222    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   10.2976    5.1334    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.7143    6.1438    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.4995    4.9344    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.7844    6.6654    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.4413    7.2633    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2139    6.1719    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    8.7863    4.9344    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   10.5112    5.9303    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    8.0718    6.1719    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.7101    4.4189    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.7850    5.3469    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.4995    4.1094    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.1589    7.4004    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.2337    5.9735    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.6711    6.9677    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    5.2139    4.5219    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.6084    4.5290    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.2961    7.3759    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.8938    6.2300    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  4  3  1  0  0  0  0
  5  3  1  0  0  0  0
  6  4  1  0  0  0  0
  7  5  1  0  0  0  0
 10  8  1  0  0  0  0
 11  8  1  0  0  0  0
 12  6  1  0  0  0  0
  9 13  1  6  0  0  0
 14  1  1  0  0  0  0
 14  2  1  0  0  0  0
 14  9  1  0  0  0  0
  6 15  1  6  0  0  0
 16  7  2  0  0  0  0
  8 16  1  1  0  0  0
 17  9  1  0  0  0  0
 17 10  1  0  0  0  0
 17 11  1  0  0  0  0
  7 18  1  4  0  0  0
 19 10  2  0  0  0  0
 20 12  2  0  0  0  0
 21 12  1  0  0  0  0
 22 13  2  0  0  0  0
 23 13  1  0  0  0  0
 24 11  1  0  0  0  0
 24 14  1  0  0  0  0
  6 25  1  6  0  0  0
  8 26  1  6  0  0  0
  9 27  1  1  0  0  0
 11 28  1  6  0  0  0
M  END


  Mrv0541 05041405552D          

 28 29  0  0  1  0            999 V2000
   11.1332    7.7127    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.0668    7.9984    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.6429    5.3469    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9284    4.9344    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.3573    4.9344    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2139    5.3469    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    8.0718    5.3469    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.5008    5.3469    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   10.9605    6.6222    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   10.2976    5.1334    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.7143    6.1438    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.4995    4.9344    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.7844    6.6654    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.4413    7.2633    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2139    6.1719    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    8.7863    4.9344    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   10.5112    5.9303    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    8.0718    6.1719    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.7101    4.4189    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.7850    5.3469    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.4995    4.1094    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.1589    7.4004    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.2337    5.9735    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.6711    6.9677    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    5.2139    4.5219    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.6084    4.5290    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.2961    7.3759    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.8938    6.2300    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  4  3  1  0  0  0  0
  5  3  1  0  0  0  0
  6  4  1  0  0  0  0
  7  5  1  0  0  0  0
 10  8  1  0  0  0  0
 11  8  1  0  0  0  0
 12  6  1  0  0  0  0
  9 13  1  6  0  0  0
 14  1  1  0  0  0  0
 14  2  1  0  0  0  0
 14  9  1  0  0  0  0
  6 15  1  6  0  0  0
 16  7  2  0  0  0  0
  8 16  1  1  0  0  0
 17  9  1  0  0  0  0
 17 10  1  0  0  0  0
 17 11  1  0  0  0  0
  7 18  1  4  0  0  0
 19 10  2  0  0  0  0
 20 12  2  0  0  0  0
 21 12  1  0  0  0  0
 22 13  2  0  0  0  0
 23 13  1  0  0  0  0
 24 11  1  0  0  0  0
 24 14  1  0  0  0  0
  6 25  1  6  0  0  0
  8 26  1  6  0  0  0
  9 27  1  1  0  0  0
 11 28  1  6  0  0  0
M  END
> <DATABASE_ID>
MMDBc0053378

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@](N)(CCCC(O)=N[C@]1([H])C(=O)N2[C@]1([H])SC(C)(C)[C@]2([H])C(O)=O)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C14H21N3O6S/c1-14(2)9(13(22)23)17-10(19)8(11(17)24-14)16-7(18)5-3-4-6(15)12(20)21/h6,8-9,11H,3-5,15H2,1-2H3,(H,16,18)(H,20,21)(H,22,23)/t6-,8+,9-,11+/m0/s1

> <INCHI_KEY>
MIFYHUACUWQUKT-GTQWGBSQSA-N

> <FORMULA>
C14H21N3O6S

> <MOLECULAR_WEIGHT>
359.398

> <EXACT_MASS>
359.115106109

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_AVERAGE_POLARIZABILITY>
35.261581336218

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S,5R,6R)-6-{[(5S)-5-amino-5-carboxy-1-hydroxypentylidene]amino}-3,3-dimethyl-7-oxo-4-thia-1-azabicyclo[3.2.0]heptane-2-carboxylic acid

> <ALOGPS_LOGP>
-1.94

> <JCHEM_LOGP>
-2.579195653564068

> <ALOGPS_LOGS>
-2.66

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
3.584446292870892

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.8261052662223594

> <JCHEM_PKA_STRONGEST_BASIC>
9.529587376751913

> <JCHEM_POLAR_SURFACE_AREA>
153.51999999999998

> <JCHEM_REFRACTIVITY>
83.57259999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
7.91e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2S,5R,6R)-6-{[(5S)-5-amino-5-carboxy-1-hydroxypentylidene]amino}-3,3-dimethyl-7-oxo-4-thia-1-azabicyclo[3.2.0]heptane-2-carboxylic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 04-MAY-14   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-MAY-14         0                                  
HETATM    1  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   15  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   16  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   17  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   18  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   24  S   UNK     0       0.000   0.000   0.000  0.00  0.00           S+0
HETATM   25  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   26  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   27  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   28  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
CONECT    1   14                                                            
CONECT    2   14                                                            
CONECT    3    4    5                                                       
CONECT    4    3    6                                                       
CONECT    5    3    7                                                       
CONECT    6    4   12   15   25                                             
CONECT    7    5   16   18                                                  
CONECT    8   10   11   16   26                                             
CONECT    9   13   14   17   27                                             
CONECT   10    8   17   19                                                  
CONECT   11    8   17   24   28                                             
CONECT   12    6   20   21                                                  
CONECT   13    9   22   23                                                  
CONECT   14    1    2    9   24                                             
CONECT   15    6                                                            
CONECT   16    7    8                                                       
CONECT   17    9   10   11                                                  
CONECT   18    7                                                            
CONECT   19   10                                                            
CONECT   20   12                                                            
CONECT   21   12                                                            
CONECT   22   13                                                            
CONECT   23   13                                                            
CONECT   24   11   14                                                       
CONECT   25    6                                                            
CONECT   26    8                                                            
CONECT   27    9                                                            
CONECT   28   11                                                            
MASTER        0    0    0    0    0    0    0    0   28    0   58    0
END

Synonyms

Value	Source
(2S,5R,6R)-6-[(5S)-5-Amino-5-carboxypentanamido]-3,3-dimethyl-7-oxo-4-thia-1-azabicyclo[3.2.0]heptane-2-carboxylic acid	ChEBI
(2S,5R,6R)-6-[(5S)-5-Amino-5-carboxypentanamido]-3,3-dimethyl-7-oxo-4-thia-1-azabicyclo[3.2.0]heptane-2-carboxylate	Generator
Penicillin N, (2S-(2alpha,5alpha,6beta(r*)))-isomer	MeSH
Penicillin N, monopotassium salt, (2S-(2alpha,5alpha,6beta(r*)))-isomer	MeSH
Penicillin N	MeSH
Penicillin N, potassium salt, (2S-(2alpha,5alpha,6beta(r*)))-isomer	MeSH
D-4-amino-4-Carboxybutyl penicillanic acid	MeSH
Adicillin	MeSH
Cephalosporin N	MeSH
Penicillin N, potassium salt, (2S-(2alpha,5alpha,6beta(s*)))-isomer	MeSH

Molecular Formula

C₁₄H₂₁N₃O₆S

Average Mass

359.398

Monoisotopic Mass

359.115106109

IUPAC Name

(2S,5R,6R)-6-{[(5S)-5-amino-5-carboxy-1-hydroxypentylidene]amino}-3,3-dimethyl-7-oxo-4-thia-1-azabicyclo[3.2.0]heptane-2-carboxylic acid

Traditional Name

(2S,5R,6R)-6-{[(5S)-5-amino-5-carboxy-1-hydroxypentylidene]amino}-3,3-dimethyl-7-oxo-4-thia-1-azabicyclo[3.2.0]heptane-2-carboxylic acid

CAS Registry Number

Not Available

SMILES

[H][C@](N)(CCCC(O)=N[C@]1([H])C(=O)N2[C@]1([H])SC(C)(C)[C@]2([H])C(O)=O)C(O)=O

InChI Identifier

InChI=1S/C14H21N3O6S/c1-14(2)9(13(22)23)17-10(19)8(11(17)24-14)16-7(18)5-3-4-6(15)12(20)21/h6,8-9,11H,3-5,15H2,1-2H3,(H,16,18)(H,20,21)(H,22,23)/t6-,8+,9-,11+/m0/s1

InChI Key

MIFYHUACUWQUKT-GTQWGBSQSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as aminobenzoic acids. These are benzoic acids containing an amine group attached to the benzene moiety.

Kingdom

Organic compounds

Super Class

Benzenoids

Class

Benzene and substituted derivatives

Sub Class

Benzoic acids and derivatives

Direct Parent

Aminobenzoic acids

Alternative Parents

Substituents

Aminobenzoic acid
Monosaccharide phosphate
Benzoic acid
Benzoyl
Phenylalkylamine
Aniline or substituted anilines
Monoalkyl phosphate
Secondary aliphatic/aromatic amine
Monosaccharide
Organic phosphoric acid derivative
Phosphoric acid ester
Alkyl phosphate
1,3-aminoalcohol
Vinylogous amide
Secondary alcohol
Amino acid or derivatives
Amino acid
1,2-aminoalcohol
Monocarboxylic acid or derivatives
Carboxylic acid
Carboxylic acid derivative
Secondary amine
Polyol
Hydrocarbon derivative
Alcohol
Organic oxide
Organopnictogen compound
Organic oxygen compound
Organic nitrogen compound
Organonitrogen compound
Organooxygen compound
Amine
Aromatic homomonocyclic compound

Molecular Framework

Aromatic homomonocyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	0.79 g/L	ALOGPS
logP	-1.9	ALOGPS
logP	-2.6	ChemAxon
logS	-2.7	ALOGPS
pKa (Strongest Acidic)	1.83	ChemAxon
pKa (Strongest Basic)	9.53	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	8	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	153.52 Å²	ChemAxon
Rotatable Bond Count	7	ChemAxon
Refractivity	83.57 m³·mol⁻¹	ChemAxon
Polarizability	35.26 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

Spectrum Type	Description	Splash Key	Deposition Date	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-01ox-9225000000-979f250fa6dd5461f291	2017-08-28	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-03di-2967000000-3279839af9a8f6bae12c	2017-07-25	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-08fr-1941000000-f4548435c7b849f41fcd	2017-07-25	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0bt9-9620000000-dec3d9df9510caa9b767	2017-07-25	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-014i-0291000000-b75d7b3b04d80a18f555	2017-07-26	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-014i-0491000000-183d36984deff6fe4346	2017-07-26	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0103-9320000000-73a968f92dc318f3b0ea	2017-07-26	View Spectrum

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
Bacteria	Actinobacteria	6
Eukaryota/Fungi	Ascomycota	4	Human feces
Bacteria	Bacteroidetes	2	Human
Bacteria	Proteobacteria	1

Exposure Sources

Source Type	Source Sub-type	Species	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

DB03550

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

C00000778

Chemspider ID

Not Available

KEGG Compound ID

C05557

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

440723

PDB ID

Not Available

ChEBI ID

18165

Food Biomarker Ontology

Not Available

References

Synthesis Reference

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 Isopenicillin N (MMDBc0053378)

MOL for #<Metabolite:0x00007f46dc5f4220>

3D MOL for #<Metabolite:0x00007f46dc5f4220>

3D SDF for #<Metabolite:0x00007f46dc5f4220>

3D-SDF for #<Metabolite:0x00007f46dc5f4220>

PDB for #<Metabolite:0x00007f46dc5f4220>

3D PDB for #<Metabolite:0x00007f46dc5f4220>

SMILES for #<Metabolite:0x00007f46dc5f4220>

INCHI for #<Metabolite:0x00007f46dc5f4220>

Structure for #<Metabolite:0x00007f46dc5f4220>

3D Structure for #<Metabolite:0x00007f46dc5f4220>