MiMeDB: Showing metabocard for Deacetylcephalosporin C (MMDBc0052988)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2022-05-16 21:11:05 UTC

Update Date

2022-09-01 02:19:38 UTC

Metabolite ID

MMDBc0052988

Metabolite Identification

Common Name

Deacetylcephalosporin C

Description

Structure

MOL SDF PDB SMILES InChI

 
  Mrv1533006041520192D          
 
 26 27  0  0  1  0            999 V2000
   16.8640  -10.7806    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   16.8640   -9.9556    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   17.5755  -11.2082    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.0390  -10.7806    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.0390   -9.9556    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   17.5755   -9.5468    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
   18.2985  -10.7882    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.5680  -11.9068    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.4562  -11.3635    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.0090   -9.8259    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   18.2985   -9.9556    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   19.0100  -11.2007    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.8527  -12.3117    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   18.2795  -12.3231    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   14.0444   -9.2024    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   19.7253  -10.7882    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.3330   -9.6150    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.0444   -8.4617    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.6176   -9.2024    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.9061   -9.6150    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.1946   -9.2024    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   10.4794   -9.6150    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.1946   -8.5039    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    9.7678   -9.1987    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.4831  -10.4363    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.8640   -9.1764    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  1  0  0  0  0
  1  4  1  0  0  0  0
  2  5  1  0  0  0  0
  2  6  1  0  0  0  0
  3  7  2  0  0  0  0
  3  8  1  0  0  0  0
  4  9  2  0  0  0  0
  5 10  1  1  0  0  0
  6 11  1  0  0  0  0
  7 12  1  0  0  0  0
  8 13  1  0  0  0  0
  8 14  2  0  0  0  0
 10 15  1  0  0  0  0
 12 16  1  0  0  0  0
 15 17  1  0  0  0  0
 15 18  2  0  0  0  0
 17 19  1  0  0  0  0
 19 20  1  0  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
 21 23  1  6  0  0  0
 22 24  1  0  0  0  0
 22 25  2  0  0  0  0
  4  5  1  0  0  0  0
  7 11  1  0  0  0  0
  2 26  1  6  0  0  0
M  END

 
  Mrv1533006041520192D          
 
 26 27  0  0  1  0            999 V2000
   16.8640  -10.7806    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   16.8640   -9.9556    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   17.5755  -11.2082    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.0390  -10.7806    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.0390   -9.9556    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   17.5755   -9.5468    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
   18.2985  -10.7882    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.5680  -11.9068    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.4562  -11.3635    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.0090   -9.8259    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   18.2985   -9.9556    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   19.0100  -11.2007    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.8527  -12.3117    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   18.2795  -12.3231    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   14.0444   -9.2024    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   19.7253  -10.7882    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.3330   -9.6150    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.0444   -8.4617    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.6176   -9.2024    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.9061   -9.6150    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.1946   -9.2024    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   10.4794   -9.6150    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.1946   -8.5039    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    9.7678   -9.1987    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.4831  -10.4363    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.8640   -9.1764    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  1  0  0  0  0
  1  4  1  0  0  0  0
  2  5  1  0  0  0  0
  2  6  1  0  0  0  0
  3  7  2  0  0  0  0
  3  8  1  0  0  0  0
  4  9  2  0  0  0  0
  5 10  1  1  0  0  0
  6 11  1  0  0  0  0
  7 12  1  0  0  0  0
  8 13  1  0  0  0  0
  8 14  2  0  0  0  0
 10 15  1  0  0  0  0
 12 16  1  0  0  0  0
 15 17  1  0  0  0  0
 15 18  2  0  0  0  0
 17 19  1  0  0  0  0
 19 20  1  0  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
 21 23  1  6  0  0  0
 22 24  1  0  0  0  0
 22 25  2  0  0  0  0
  4  5  1  0  0  0  0
  7 11  1  0  0  0  0
  2 26  1  6  0  0  0
M  END
> <DATABASE_ID>
MMDBc0052988

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@]12SCC(CO)=C(N1C(=O)[C@H]2NC(=O)CCC[C@@H](N)C(O)=O)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C14H19N3O7S/c15-7(13(21)22)2-1-3-8(19)16-9-11(20)17-10(14(23)24)6(4-18)5-25-12(9)17/h7,9,12,18H,1-5,15H2,(H,16,19)(H,21,22)(H,23,24)/t7-,9-,12-/m1/s1

> <INCHI_KEY>
XWCFYHBHOFBVIV-JWKOBGCHSA-N

> <FORMULA>
C14H19N3O7S

> <MOLECULAR_WEIGHT>
373.38

> <EXACT_MASS>
373.094371138

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_ATOM_COUNT>
44

> <JCHEM_AVERAGE_POLARIZABILITY>
35.84761321295444

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(6R,7R)-7-[(5R)-5-amino-5-carboxypentanamido]-3-(hydroxymethyl)-8-oxo-5-thia-1-azabicyclo[4.2.0]oct-2-ene-2-carboxylic acid

> <ALOGPS_LOGP>
-2.74

> <JCHEM_LOGP>
-4.794395895902001

> <ALOGPS_LOGS>
-1.79

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
3.713488373083261

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.8378710714191882

> <JCHEM_PKA_STRONGEST_BASIC>
9.224842367684785

> <JCHEM_POLAR_SURFACE_AREA>
170.26000000000002

> <JCHEM_REFRACTIVITY>
86.27569999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.07e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
deacetylcephalosporin C

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 04-JUN-15   NONE
TITLE     NULL                                                        
COMPND    MOLECULE:                                                   
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-JUN-15         0                                  
HETATM    1  N   UNK     0      31.480 -20.124   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0      31.480 -18.584   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      32.808 -20.922   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      29.940 -20.124   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      29.940 -18.584   0.000  0.00  0.00           C+0
HETATM    6  S   UNK     0      32.808 -17.821   0.000  0.00  0.00           S+0
HETATM    7  C   UNK     0      34.157 -20.138   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      32.794 -22.226   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0      28.852 -21.212   0.000  0.00  0.00           O+0
HETATM   10  N   UNK     0      28.017 -18.342   0.000  0.00  0.00           N+0
HETATM   11  C   UNK     0      34.157 -18.584   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      35.485 -20.908   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0      31.458 -22.982   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0      34.122 -23.003   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0      26.216 -17.178   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0      36.821 -20.138   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0      24.888 -17.948   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0      26.216 -15.795   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0      23.553 -17.178   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      22.225 -17.948   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      20.897 -17.178   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      19.562 -17.948   0.000  0.00  0.00           C+0
HETATM   23  N   UNK     0      20.897 -15.874   0.000  0.00  0.00           N+0
HETATM   24  O   UNK     0      18.233 -17.171   0.000  0.00  0.00           O+0
HETATM   25  O   UNK     0      19.568 -19.481   0.000  0.00  0.00           O+0
HETATM   26  H   UNK     0      31.480 -17.129   0.000  0.00  0.00           H+0
CONECT    1    2    3    4                                                  
CONECT    2    1    5    6   26                                             
CONECT    3    1    7    8                                                  
CONECT    4    1    9    5                                                  
CONECT    5    2   10    4                                                  
CONECT    6    2   11                                                       
CONECT    7    3   12   11                                                  
CONECT    8    3   13   14                                                  
CONECT    9    4                                                            
CONECT   10    5   15                                                       
CONECT   11    6    7                                                       
CONECT   12    7   16                                                       
CONECT   13    8                                                            
CONECT   14    8                                                            
CONECT   15   10   17   18                                                  
CONECT   16   12                                                            
CONECT   17   15   19                                                       
CONECT   18   15                                                            
CONECT   19   17   20                                                       
CONECT   20   19   21                                                       
CONECT   21   20   22   23                                                  
CONECT   22   21   24   25                                                  
CONECT   23   21                                                            
CONECT   24   22                                                            
CONECT   25   22                                                            
CONECT   26    2                                                            
MASTER        0    0    0    0    0    0    0    0   26    0   54    0
END

Synonyms

Value	Source
Deacetylcephalosporin C, sodium salt	MeSH
Deacetylcephalosporin C, (6R-(6alpha,7beta))-isomer	MeSH
Deacetylcephalosporin C, potassium salt	MeSH
Deacetylcephalosporin C, monopotassium salt	MeSH
Deacetylcephalosporin C, monosodium salt	MeSH

Molecular Formula

C₁₄H₁₉N₃O₇S

Average Mass

373.38

Monoisotopic Mass

373.094371138

IUPAC Name

(6R,7R)-7-[(5R)-5-amino-5-carboxypentanamido]-3-(hydroxymethyl)-8-oxo-5-thia-1-azabicyclo[4.2.0]oct-2-ene-2-carboxylic acid

Traditional Name

deacetylcephalosporin C

CAS Registry Number

Not Available

SMILES

[H][C@]12SCC(CO)=C(N1C(=O)[C@H]2NC(=O)CCC[C@@H](N)C(O)=O)C(O)=O

InChI Identifier

InChI=1S/C14H19N3O7S/c15-7(13(21)22)2-1-3-8(19)16-9-11(20)17-10(14(23)24)6(4-18)5-25-12(9)17/h7,9,12,18H,1-5,15H2,(H,16,19)(H,21,22)(H,23,24)/t7-,9-,12-/m1/s1

InChI Key

XWCFYHBHOFBVIV-JWKOBGCHSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as cephalosporins. Cephalosporins are compounds containing a 1,2-thiazine fused to a 2-azetidinone to for a oxo-5-thia-1-azabicyclo[4.2.0]Oct-2-ene-2-carboxylic acid moiety or a derivative thereof.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Lactams

Sub Class

Beta lactams

Direct Parent

Cephalosporins

Alternative Parents

Substituents

Cephalosporin
N-acyl-alpha amino acid or derivatives
Alpha-amino acid
Alpha-amino acid or derivatives
D-alpha-amino acid
Medium-chain fatty acid
Heterocyclic fatty acid
Hydroxy fatty acid
Dicarboxylic acid or derivatives
Fatty amide
Fatty acyl
Meta-thiazine
N-acyl-amine
Tertiary carboxylic acid amide
Amino acid or derivatives
Azetidine
Carboxamide group
Amino acid
Secondary carboxylic acid amide
Carboxylic acid derivative
Carboxylic acid
Azacycle
Dialkylthioether
Hemithioaminal
Thioether
Organic nitrogen compound
Organopnictogen compound
Primary amine
Organic oxygen compound
Carbonyl group
Alcohol
Hydrocarbon derivative
Primary alcohol
Organooxygen compound
Organonitrogen compound
Primary aliphatic amine
Amine
Organic oxide
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic heteropolycyclic compounds

External Descriptors

3-hydroxymethylcephalosporin (CHEBI:18065 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	6.07 g/L	ALOGPS
logP	-2.7	ALOGPS
logP	-4.8	ChemAxon
logS	-1.8	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	5	ChemAxon
Polar Surface Area	170.26 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	86.28 m³·mol⁻¹	ChemAxon
Polarizability	35.85 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 (TMS_1_2) - 70eV, Positive	Not Available	2022-08-08	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-074i-0539000000-8ec7b2559cc03175f883	2019-02-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0c29-1923000000-4764ac595a72cb1b6a95	2019-02-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-00xr-6921000000-729345370f0c55d26d35	2019-02-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0002-0924000000-5581c1a3e754fe7cfc6b	2019-02-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-014j-1975000000-f725eee01994c4899130	2019-02-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-00kf-9430000000-3fbcac6646627b8ca198	2019-02-23	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	2
Eukaryota/Fungi	Ascomycota	1
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

C03112

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

Not Available

PDB ID

Not Available

ChEBI ID

18065

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 Deacetylcephalosporin C (MMDBc0052988)

MOL for #<Metabolite:0x00007fecc0044430>

3D MOL for #<Metabolite:0x00007fecc0044430>

3D SDF for #<Metabolite:0x00007fecc0044430>

3D-SDF for #<Metabolite:0x00007fecc0044430>

PDB for #<Metabolite:0x00007fecc0044430>

3D PDB for #<Metabolite:0x00007fecc0044430>

SMILES for #<Metabolite:0x00007fecc0044430>

INCHI for #<Metabolite:0x00007fecc0044430>

Structure for #<Metabolite:0x00007fecc0044430>

3D Structure for #<Metabolite:0x00007fecc0044430>