Hmdb loader
Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-09-06 15:16:51 UTC
Update Date2022-03-07 02:51:56 UTC
HMDB IDHMDB0015294
Secondary Accession Numbers
  • HMDB15294
Metabolite Identification
Common NameAmdinocillin
DescriptionAmdinocillin is only found in individuals that have used or taken this drug. It is an amidinopenicillanic acid derivative with broad spectrum antibacterial action. It is poorly absorbed if given orally and is used in urinary infections and typhus. [PubChem]Amdinocillin is a stong and specific antagonist of Penicillin Binding Protein-2 (PBP 2). It is active against gram negative bacteria, preventing cell wall synthesis by inhibiting the activity of PBP2. PBP2 is a peptidoglycan elongation initiating enzyme. Peptidoglycan is a polymer of sugars and amino acids that is the main component of bacterial cell walls.
Structure
Data?1582753280
Synonyms
ValueSource
(2S,5R,6R)-6-[(Azepan-1-ylmethylidene)amino]-3,3-dimethyl-7-oxo-4-thia-1-azabicyclo[3.2.0]heptane-2-carboxylic acidChEBI
CoactinChEBI
MecilinamoChEBI
MecillinamumChEBI
Penicillin HXChEBI
(2S,5R,6R)-6-[(Azepan-1-ylmethylidene)amino]-3,3-dimethyl-7-oxo-4-thia-1-azabicyclo[3.2.0]heptane-2-carboxylateGenerator
MecillinamHMDB
AmdinocillinChEBI
Chemical FormulaC15H23N3O3S
Average Molecular Weight325.426
Monoisotopic Molecular Weight325.146012307
IUPAC Name(2S,5R,6R)-6-[(azepan-1-ylmethylidene)amino]-3,3-dimethyl-7-oxo-4-thia-1-azabicyclo[3.2.0]heptane-2-carboxylic acid
Traditional Namemecillinam
CAS Registry Number32887-01-7
SMILES
[H]C(=N[C@@H]1C(=O)N2[C@@H](C(O)=O)C(C)(C)S[C@]12[H])N1CCCCCC1
InChI Identifier
InChI=1S/C15H23N3O3S/c1-15(2)11(14(20)21)18-12(19)10(13(18)22-15)16-9-17-7-5-3-4-6-8-17/h9-11,13H,3-8H2,1-2H3,(H,20,21)/t10-,11+,13-/m1/s1
InChI KeyBWWVAEOLVKTZFQ-NTZNESFSSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as alpha amino acids and derivatives. These are amino acids in which the amino group is attached to the carbon atom immediately adjacent to the carboxylate group (alpha carbon), or a derivative thereof.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassCarboxylic acids and derivatives
Sub ClassAmino acids, peptides, and analogues
Direct ParentAlpha amino acids and derivatives
Alternative Parents
Substituents
  • Alpha-amino acid or derivatives
  • Penam
  • Azepane
  • Beta-lactam
  • Tertiary carboxylic acid amide
  • Thiazolidine
  • Azetidine
  • Carboxamide group
  • Lactam
  • Amidine
  • Formamidine
  • Carboxylic acid amidine
  • Carboxylic acid
  • Monocarboxylic acid or derivatives
  • Azacycle
  • Organoheterocyclic compound
  • Dialkylthioether
  • Thioether
  • Organic 1,3-dipolar compound
  • Propargyl-type 1,3-dipolar organic compound
  • Carboximidamide
  • Hemithioaminal
  • Organooxygen compound
  • Organopnictogen compound
  • Carbonyl group
  • Organic oxide
  • Organic nitrogen compound
  • Hydrocarbon derivative
  • Organic oxygen compound
  • Organonitrogen compound
  • Aliphatic heteropolycyclic compound
Molecular FrameworkAliphatic heteropolycyclic compounds
External Descriptors
Ontology
Not AvailableNot Available
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting Point156 °CNot Available
Boiling PointNot AvailableNot Available
Water Solubility0.98 g/LNot Available
LogP1.3Not Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility0.98 g/LALOGPS
logP1.41ALOGPS
logP-0.55ChemAxon
logS-2.5ALOGPS
pKa (Strongest Acidic)3.3ChemAxon
pKa (Strongest Basic)7.92ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area73.21 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity84.31 m³·mol⁻¹ChemAxon
Polarizability34.18 ųChemAxon
Number of Rings3ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DarkChem[M+H]+173.49831661259
DarkChem[M-H]-165.56531661259
DeepCCS[M-2H]-221.96130932474
DeepCCS[M+Na]+196.63130932474
AllCCS[M+H]+174.232859911
AllCCS[M+H-H2O]+171.432859911
AllCCS[M+NH4]+176.932859911
AllCCS[M+Na]+177.632859911
AllCCS[M-H]-176.932859911
AllCCS[M+Na-2H]-177.132859911
AllCCS[M+HCOO]-177.332859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
Amdinocillin[H]C(=N[C@@H]1C(=O)N2[C@@H](C(O)=O)C(C)(C)S[C@]12[H])N1CCCCCC13432.4Standard polar33892256
Amdinocillin[H]C(=N[C@@H]1C(=O)N2[C@@H](C(O)=O)C(C)(C)S[C@]12[H])N1CCCCCC12629.6Standard non polar33892256
Amdinocillin[H]C(=N[C@@H]1C(=O)N2[C@@H](C(O)=O)C(C)(C)S[C@]12[H])N1CCCCCC12692.3Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
Amdinocillin,1TMS,isomer #1CC1(C)S[C@@H]2[C@H](N=CN3CCCCCC3)C(=O)N2[C@H]1C(=O)O[Si](C)(C)C2581.7Semi standard non polar33892256
Amdinocillin,1TBDMS,isomer #1CC1(C)S[C@@H]2[C@H](N=CN3CCCCCC3)C(=O)N2[C@H]1C(=O)O[Si](C)(C)C(C)(C)C2779.4Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Amdinocillin GC-MS (Non-derivatized) - 70eV, Positivesplash10-00kg-9771000000-9b076aefae04fb4accc72017-09-01Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Amdinocillin GC-MS (1 TMS) - 70eV, Positivesplash10-0aw9-9426000000-3af5eac2474617cff9442017-10-06Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Amdinocillin GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Experimental LC-MS/MSLC-MS/MS Spectrum - Amdinocillin LC-ESI-qTof , Positive-QTOFsplash10-004i-0209000000-8ccc98a85688a2a0d3da2017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Amdinocillin , positive-QTOFsplash10-004i-0209000000-8ccc98a85688a2a0d3da2017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Amdinocillin 35V, Positive-QTOFsplash10-004i-2945000000-e8db09b7ad3ac5a56bc72021-09-20HMDB team, MONAView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Amdinocillin 10V, Positive-QTOFsplash10-0400-0902000000-6ad7570ceb8947255ae22017-07-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Amdinocillin 20V, Positive-QTOFsplash10-03xr-0900000000-852ea92becf7c8c57efc2017-07-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Amdinocillin 40V, Positive-QTOFsplash10-03yl-9700000000-f94e9fae3a0ab03ab4812017-07-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Amdinocillin 10V, Negative-QTOFsplash10-001i-0920000000-f8ce04a608c25649c7c42017-07-26Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Amdinocillin 20V, Negative-QTOFsplash10-001i-1930000000-3ba8b20b5ea1b00213942017-07-26Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Amdinocillin 40V, Negative-QTOFsplash10-0059-9410000000-9e76238ee6c6023f89032017-07-26Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Amdinocillin 10V, Positive-QTOFsplash10-004i-0309000000-bb0323e9d2e52cc380822021-10-11Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Amdinocillin 20V, Positive-QTOFsplash10-002r-0912000000-b0f50e5a14d1e63910872021-10-11Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Amdinocillin 40V, Positive-QTOFsplash10-03g1-2910000000-129c7c23a11f2bcee60d2021-10-11Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Amdinocillin 10V, Negative-QTOFsplash10-0002-0090000000-fce2a606f19d61a93af52021-10-11Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Amdinocillin 20V, Negative-QTOFsplash10-0002-0890000000-47c89d1c549ec24069f42021-10-11Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Amdinocillin 40V, Negative-QTOFsplash10-00xu-6950000000-e944d9173c89ff24f1072021-10-11Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Biological Properties
Cellular Locations
  • Membrane
Biospecimen Locations
  • Blood
  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodExpected but not QuantifiedNot QuantifiedNot AvailableNot AvailableTaking drug identified by DrugBank entry DB01163 details
UrineExpected but not QuantifiedNot QuantifiedNot AvailableNot AvailableTaking drug identified by DrugBank entry DB01163 details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDDB01163
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID10482146
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkMecillinam
METLIN IDNot Available
PubChem Compound36273
PDB IDNot Available
ChEBI ID51208
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Neu HC: Penicillin-binding proteins and role of amdinocillin in causing bacterial cell death. Am J Med. 1983 Aug 29;75(2A):9-20. [PubMed:6311012 ]