MiMeDB: Showing metabocard for Cephalosporin C (MMDBc0009798)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-05-15 02:12:48 UTC

Update Date

2022-08-31 06:30:45 UTC

Metabolite ID

MMDBc0009798

Metabolite Identification

Common Name

Cephalosporin C

Description

3-[(acetyloxy)methyl]-7-[(5-amino-5-carboxy-1-hydroxypentylidene)amino]-8-oxo-5-thia-1-azabicyclo[4.2.0]oct-2-ene-2-carboxylic acid belongs to the class of organic compounds known as cephalosporin 3'-esters. These are cephalosporins that are esterified at the 3'-position. 3-[(acetyloxy)methyl]-7-[(5-amino-5-carboxy-1-hydroxypentylidene)amino]-8-oxo-5-thia-1-azabicyclo[4.2.0]oct-2-ene-2-carboxylic acid is a very strong basic compound (based on its pKa).

Structure

MOL SDF PDB SMILES InChI


  Mrv1533004231523552D          

 28 29  0  0  0  0            999 V2000
   -5.3501    2.6352    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7668    3.2186    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9803    4.0155    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9699    3.0050    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3865    3.5884    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5896    3.3749    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0063    3.9582    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2094    3.7447    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9959    2.9478    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5792    2.3645    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3761    2.5780    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1990    3.1614    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5155    2.7489    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.2300    3.1614    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2300    3.9864    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9444    2.7489    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6589    3.1614    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3734    2.7489    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0879    3.1614    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0879    3.9864    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.8023    2.7489    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5168    3.1614    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.8023    1.9239    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125    3.9582    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    4.6727    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2198    4.7551    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6364    5.3385    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0167    4.9687    0.0000 O   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  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
  6 11  1  0  0  0  0
  9 12  1  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
 14 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
 19 20  1  0  0  0  0
 19 21  1  0  0  0  0
 21 22  2  0  0  0  0
 21 23  1  0  0  0  0
 12 24  1  0  0  0  0
  8 24  1  0  0  0  0
 24 25  2  0  0  0  0
  7 26  1  0  0  0  0
 26 27  2  0  0  0  0
 26 28  1  0  0  0  0
M  END


  Mrv1533004231523552D          

 28 29  0  0  0  0            999 V2000
   -5.3501    2.6352    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7668    3.2186    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9803    4.0155    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9699    3.0050    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3865    3.5884    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5896    3.3749    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0063    3.9582    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2094    3.7447    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9959    2.9478    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5792    2.3645    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3761    2.5780    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1990    3.1614    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5155    2.7489    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.2300    3.1614    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2300    3.9864    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9444    2.7489    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6589    3.1614    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3734    2.7489    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0879    3.1614    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0879    3.9864    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.8023    2.7489    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5168    3.1614    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.8023    1.9239    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125    3.9582    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    4.6727    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2198    4.7551    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6364    5.3385    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0167    4.9687    0.0000 O   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  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
  6 11  1  0  0  0  0
  9 12  1  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
 14 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
 19 20  1  0  0  0  0
 19 21  1  0  0  0  0
 21 22  2  0  0  0  0
 21 23  1  0  0  0  0
 12 24  1  0  0  0  0
  8 24  1  0  0  0  0
 24 25  2  0  0  0  0
  7 26  1  0  0  0  0
 26 27  2  0  0  0  0
 26 28  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0009798

> <DATABASE_NAME>
MIME

> <SMILES>
CC(=O)OCC1=C(N2C(SC1)C(NC(=O)CCCC(N)C(O)=O)C2=O)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C16H21N3O8S/c1-7(20)27-5-8-6-28-14-11(13(22)19(14)12(8)16(25)26)18-10(21)4-2-3-9(17)15(23)24/h9,11,14H,2-6,17H2,1H3,(H,18,21)(H,23,24)(H,25,26)

> <INCHI_KEY>
HOKIDJSKDBPKTQ-UHFFFAOYSA-N

> <FORMULA>
C16H21N3O8S

> <MOLECULAR_WEIGHT>
415.42

> <EXACT_MASS>
415.104935822

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_ATOM_COUNT>
49

> <JCHEM_AVERAGE_POLARIZABILITY>
40.232348179110915

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3-[(acetyloxy)methyl]-7-(5-amino-5-carboxypentanamido)-8-oxo-5-thia-1-azabicyclo[4.2.0]oct-2-ene-2-carboxylic acid

> <ALOGPS_LOGP>
-2.18

> <JCHEM_LOGP>
-4.3573375949766895

> <ALOGPS_LOGS>
-2.27

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
3.6875050748975147

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.8375042564087951

> <JCHEM_PKA_STRONGEST_BASIC>
9.224805327069886

> <JCHEM_POLAR_SURFACE_AREA>
176.32999999999998

> <JCHEM_REFRACTIVITY>
95.42719999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
10

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.22e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
cephalosporin C

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 23-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-APR-15         0                                  
HETATM    1  C   UNK     0      -9.987   4.919   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -8.898   6.008   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0      -9.297   7.496   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0      -7.410   5.609   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0      -6.322   6.698   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -4.834   6.300   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -3.745   7.389   0.000  0.00  0.00           C+0
HETATM    8  N   UNK     0      -2.258   6.990   0.000  0.00  0.00           N+0
HETATM    9  C   UNK     0      -1.859   5.503   0.000  0.00  0.00           C+0
HETATM   10  S   UNK     0      -2.948   4.414   0.000  0.00  0.00           S+0
HETATM   11  C   UNK     0      -4.435   4.812   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -0.371   5.901   0.000  0.00  0.00           C+0
HETATM   13  N   UNK     0       0.962   5.131   0.000  0.00  0.00           N+0
HETATM   14  C   UNK     0       2.296   5.901   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0       2.296   7.441   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0       3.630   5.131   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       4.963   5.901   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       6.297   5.131   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       7.631   5.901   0.000  0.00  0.00           C+0
HETATM   20  N   UNK     0       7.631   7.441   0.000  0.00  0.00           N+0
HETATM   21  C   UNK     0       8.964   5.131   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0      10.298   5.901   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0       8.964   3.591   0.000  0.00  0.00           O+0
HETATM   24  C   UNK     0      -0.770   7.389   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0       0.000   8.722   0.000  0.00  0.00           O+0
HETATM   26  C   UNK     0      -4.144   8.876   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0      -3.055   9.965   0.000  0.00  0.00           O+0
HETATM   28  O   UNK     0      -5.631   9.275   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7   11                                                  
CONECT    7    6    8   26                                                  
CONECT    8    7    9   24                                                  
CONECT    9    8   10   12                                                  
CONECT   10    9   11                                                       
CONECT   11   10    6                                                       
CONECT   12    9   13   24                                                  
CONECT   13   12   14                                                       
CONECT   14   13   15   16                                                  
CONECT   15   14                                                            
CONECT   16   14   17                                                       
CONECT   17   16   18                                                       
CONECT   18   17   19                                                       
CONECT   19   18   20   21                                                  
CONECT   20   19                                                            
CONECT   21   19   22   23                                                  
CONECT   22   21                                                            
CONECT   23   21                                                            
CONECT   24   12    8   25                                                  
CONECT   25   24                                                            
CONECT   26    7   27   28                                                  
CONECT   27   26                                                            
CONECT   28   26                                                            
MASTER        0    0    0    0    0    0    0    0   28    0   58    0
END

Synonyms

Value	Source
3-[(Acetyloxy)methyl]-7-[(5-amino-5-carboxy-1-hydroxypentylidene)amino]-8-oxo-5-thia-1-azabicyclo[4.2.0]oct-2-ene-2-carboxylate	Generator

Molecular Formula

C₁₆H₂₁N₃O₈S

Average Mass

415.42

Monoisotopic Mass

415.104935822

IUPAC Name

3-[(acetyloxy)methyl]-7-(5-amino-5-carboxypentanamido)-8-oxo-5-thia-1-azabicyclo[4.2.0]oct-2-ene-2-carboxylic acid

Traditional Name

cephalosporin C

CAS Registry Number

Not Available

SMILES

CC(=O)OCC1=C(N2C(SC1)C(NC(=O)CCCC(N)C(O)=O)C2=O)C(O)=O

InChI Identifier

InChI=1S/C16H21N3O8S/c1-7(20)27-5-8-6-28-14-11(13(22)19(14)12(8)16(25)26)18-10(21)4-2-3-9(17)15(23)24/h9,11,14H,2-6,17H2,1H3,(H,18,21)(H,23,24)(H,25,26)

InChI Key

HOKIDJSKDBPKTQ-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as cephalosporin 3'-esters. These are cephalosporins that are esterified at the 3'-position.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Lactams

Sub Class

Beta lactams

Direct Parent

Cephalosporin 3'-esters

Alternative Parents

Substituents

Cephalosporin 3'-ester
N-acyl-alpha amino acid or derivatives
Alpha-amino acid
Alpha-amino acid or derivatives
Tricarboxylic acid or derivatives
Meta-thiazine
Fatty amide
N-acyl-amine
Fatty acyl
Tertiary carboxylic acid amide
Amino acid or derivatives
Azetidine
Carboxamide group
Carboxylic acid ester
Amino acid
Secondary carboxylic acid amide
Dialkylthioether
Hemithioaminal
Thioether
Azacycle
Carboxylic acid derivative
Carboxylic acid
Organooxygen compound
Organic oxide
Organopnictogen compound
Primary aliphatic amine
Organic oxygen compound
Carbonyl group
Primary amine
Organic nitrogen compound
Amine
Hydrocarbon derivative
Organonitrogen compound
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic heteropolycyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	2.22 g/L	ALOGPS
logP	-2.2	ALOGPS
logP	-4.4	ChemAxon
logS	-2.3	ALOGPS
pKa (Strongest Acidic)	1.84	ChemAxon
pKa (Strongest Basic)	9.22	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	8	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	176.33 Å²	ChemAxon
Rotatable Bond Count	10	ChemAxon
Refractivity	95.43 m³·mol⁻¹	ChemAxon
Polarizability	40.23 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

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
Eukaryota/Fungi	Ascomycota	2		Metabolic reconstruction
Bacteria	Firmicutes	1	Human feces
Bacteria	Thermotogae	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

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

2669

PDB ID

Not Available

ChEBI ID

Not Available

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 Cephalosporin C (MMDBc0009798)

MOL for #<Metabolite:0x00007fecae8721f0>

3D MOL for #<Metabolite:0x00007fecae8721f0>

3D SDF for #<Metabolite:0x00007fecae8721f0>

3D-SDF for #<Metabolite:0x00007fecae8721f0>

PDB for #<Metabolite:0x00007fecae8721f0>

3D PDB for #<Metabolite:0x00007fecae8721f0>

SMILES for #<Metabolite:0x00007fecae8721f0>

INCHI for #<Metabolite:0x00007fecae8721f0>

Structure for #<Metabolite:0x00007fecae8721f0>

3D Structure for #<Metabolite:0x00007fecae8721f0>