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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-09-06 15:16:50 UTC
Update Date2022-03-07 02:51:43 UTC
HMDB IDHMDB0014745
Secondary Accession Numbers
  • HMDB14745
Metabolite Identification
Common NameNafcillin
DescriptionNafcillin is only found in individuals that have used or taken this drug. It is a semi-synthetic antibiotic related to penicillin. [PubChem]Penicillinase-resistant penicillins exert a bactericidal action against penicillin-susceptible microorganisms during the state of active multiplication. All penicillins inhibit the biosynthesis of the bacterial cell wall.
Structure
Data?1582753216
Synonyms
ValueSource
(2-Ethoxy-1-naphthalenyl)penicillinChEBI
(2-Ethoxy-1-naphthyl)penicillinChEBI
(2S,5R,6R)-6-[(2-Ethoxy-1-naphthoyl)amino]-3,3-dimethyl-7-oxo-4-thia-1-azabicyclo[3.2.0]heptane-2-carboxylic acidChEBI
(2S,5R,6R)-6-[(2-Ethoxynaphthalene-1-carbonyl)amino]-3,3-dimethyl-7-oxo-4-thia-1-azabicyclo[3.2.0]heptane-2-carboxylic acidChEBI
(2S,5R,6R)-6-{[(2-ethoxynaphthalen-1-yl)carbonyl]amino}-3,3-dimethyl-7-oxo-4-thia-1-azabicyclo[3.2.0]heptane-2-carboxylic acidChEBI
6-(2-Ethoxy-1-naphthamido)penicillanic acidChEBI
NafcilinaChEBI
NafcillineChEBI
NafcillinumChEBI
NaphcillinChEBI
(2S,5R,6R)-6-[(2-Ethoxy-1-naphthoyl)amino]-3,3-dimethyl-7-oxo-4-thia-1-azabicyclo[3.2.0]heptane-2-carboxylateGenerator
(2S,5R,6R)-6-[(2-Ethoxynaphthalene-1-carbonyl)amino]-3,3-dimethyl-7-oxo-4-thia-1-azabicyclo[3.2.0]heptane-2-carboxylateGenerator
(2S,5R,6R)-6-{[(2-ethoxynaphthalen-1-yl)carbonyl]amino}-3,3-dimethyl-7-oxo-4-thia-1-azabicyclo[3.2.0]heptane-2-carboxylateGenerator
6-(2-Ethoxy-1-naphthamido)penicillanateGenerator
Nafcillin sodium saltHMDB
NafcilHMDB
Nafcillin, monosodium salt, anhydrousHMDB
Nafcillin sodiumHMDB
Nafcillin, sodiumHMDB
NaphthamidopenicillinHMDB
Sodium nafcillinHMDB
Sodium, nafcillinHMDB
Chemical FormulaC21H22N2O5S
Average Molecular Weight414.475
Monoisotopic Molecular Weight414.124942514
IUPAC Name(2S,5R,6R)-6-(2-ethoxynaphthalene-1-amido)-3,3-dimethyl-7-oxo-4-thia-1-azabicyclo[3.2.0]heptane-2-carboxylic acid
Traditional Namenafcillin
CAS Registry Number985-16-0
SMILES
[H][C@]12SC(C)(C)[C@@H](N1C(=O)[C@H]2NC(=O)C1=C(OCC)C=CC2=CC=CC=C12)C(O)=O
InChI Identifier
InChI=1S/C21H22N2O5S/c1-4-28-13-10-9-11-7-5-6-8-12(11)14(13)17(24)22-15-18(25)23-16(20(26)27)21(2,3)29-19(15)23/h5-10,15-16,19H,4H2,1-3H3,(H,22,24)(H,26,27)/t15-,16+,19-/m1/s1
InChI KeyGPXLMGHLHQJAGZ-JTDSTZFVSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as dipeptides. These are organic compounds containing a sequence of exactly two alpha-amino acids joined by a peptide bond.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassCarboxylic acids and derivatives
Sub ClassAmino acids, peptides, and analogues
Direct ParentDipeptides
Alternative Parents
Substituents
  • Alpha-dipeptide
  • Penicillin
  • 1-naphthalenecarboxylic acid or derivatives
  • N-acyl-alpha amino acid or derivatives
  • 1-naphthalenecarboxamide
  • Alpha-amino acid or derivatives
  • Naphthalene
  • Penam
  • Alkyl aryl ether
  • Benzenoid
  • Beta-lactam
  • Tertiary carboxylic acid amide
  • Thiazolidine
  • Azetidine
  • Secondary carboxylic acid amide
  • Carboxamide group
  • Lactam
  • Carboxylic acid
  • Ether
  • Azacycle
  • Monocarboxylic acid or derivatives
  • Organoheterocyclic compound
  • Dialkylthioether
  • Hemithioaminal
  • Thioether
  • Organic oxygen compound
  • Organopnictogen compound
  • Organic oxide
  • Carbonyl group
  • Hydrocarbon derivative
  • Organic nitrogen compound
  • Organonitrogen compound
  • Organooxygen compound
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External Descriptors
Ontology
Disposition

Biological location

Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water Solubility0.017 g/LNot Available
LogP3.3Not Available
Experimental Chromatographic Properties

Experimental Collision Cross Sections

Adduct TypeData SourceCCS Value (Å2)Reference
[M+H]+Not Available191.496http://allccs.zhulab.cn/database/detail?ID=AllCCS00001272
Predicted Molecular Properties
PropertyValueSource
Water Solubility0.017 g/LALOGPS
logP3.21ALOGPS
logP2.29ChemAxon
logS-4.4ALOGPS
pKa (Strongest Acidic)3.31ChemAxon
pKa (Strongest Basic)-1.6ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area95.94 ŲChemAxon
Rotatable Bond Count5ChemAxon
Refractivity108.14 m³·mol⁻¹ChemAxon
Polarizability42.22 ųChemAxon
Number of Rings4ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DarkChem[M+H]+193.13131661259
DarkChem[M-H]-194.7131661259
DeepCCS[M-2H]-221.13130932474
DeepCCS[M+Na]+196.55630932474

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
Nafcillin[H][C@]12SC(C)(C)[C@@H](N1C(=O)[C@H]2NC(=O)C1=C(OCC)C=CC2=CC=CC=C12)C(O)=O4785.8Standard polar33892256
Nafcillin[H][C@]12SC(C)(C)[C@@H](N1C(=O)[C@H]2NC(=O)C1=C(OCC)C=CC2=CC=CC=C12)C(O)=O2967.7Standard non polar33892256
Nafcillin[H][C@]12SC(C)(C)[C@@H](N1C(=O)[C@H]2NC(=O)C1=C(OCC)C=CC2=CC=CC=C12)C(O)=O3524.5Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
Nafcillin,1TMS,isomer #1CCOC1=CC=C2C=CC=CC2=C1C(=O)N[C@@H]1C(=O)N2[C@@H](C(=O)O[Si](C)(C)C)C(C)(C)S[C@H]123352.5Semi standard non polar33892256
Nafcillin,1TMS,isomer #2CCOC1=CC=C2C=CC=CC2=C1C(=O)N([C@@H]1C(=O)N2[C@@H](C(=O)O)C(C)(C)S[C@H]12)[Si](C)(C)C3331.2Semi standard non polar33892256
Nafcillin,2TMS,isomer #1CCOC1=CC=C2C=CC=CC2=C1C(=O)N([C@@H]1C(=O)N2[C@@H](C(=O)O[Si](C)(C)C)C(C)(C)S[C@H]12)[Si](C)(C)C3292.0Semi standard non polar33892256
Nafcillin,2TMS,isomer #1CCOC1=CC=C2C=CC=CC2=C1C(=O)N([C@@H]1C(=O)N2[C@@H](C(=O)O[Si](C)(C)C)C(C)(C)S[C@H]12)[Si](C)(C)C3232.1Standard non polar33892256
Nafcillin,2TMS,isomer #1CCOC1=CC=C2C=CC=CC2=C1C(=O)N([C@@H]1C(=O)N2[C@@H](C(=O)O[Si](C)(C)C)C(C)(C)S[C@H]12)[Si](C)(C)C3960.8Standard polar33892256
Nafcillin,1TBDMS,isomer #1CCOC1=CC=C2C=CC=CC2=C1C(=O)N[C@@H]1C(=O)N2[C@@H](C(=O)O[Si](C)(C)C(C)(C)C)C(C)(C)S[C@H]123592.7Semi standard non polar33892256
Nafcillin,1TBDMS,isomer #2CCOC1=CC=C2C=CC=CC2=C1C(=O)N([C@@H]1C(=O)N2[C@@H](C(=O)O)C(C)(C)S[C@H]12)[Si](C)(C)C(C)(C)C3541.0Semi standard non polar33892256
Nafcillin,2TBDMS,isomer #1CCOC1=CC=C2C=CC=CC2=C1C(=O)N([C@@H]1C(=O)N2[C@@H](C(=O)O[Si](C)(C)C(C)(C)C)C(C)(C)S[C@H]12)[Si](C)(C)C(C)(C)C3692.5Semi standard non polar33892256
Nafcillin,2TBDMS,isomer #1CCOC1=CC=C2C=CC=CC2=C1C(=O)N([C@@H]1C(=O)N2[C@@H](C(=O)O[Si](C)(C)C(C)(C)C)C(C)(C)S[C@H]12)[Si](C)(C)C(C)(C)C3672.5Standard non polar33892256
Nafcillin,2TBDMS,isomer #1CCOC1=CC=C2C=CC=CC2=C1C(=O)N([C@@H]1C(=O)N2[C@@H](C(=O)O[Si](C)(C)C(C)(C)C)C(C)(C)S[C@H]12)[Si](C)(C)C(C)(C)C4099.4Standard polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Nafcillin GC-MS (Non-derivatized) - 70eV, Positivesplash10-00dv-6559000000-476ab0db07d5480232f42017-09-01Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Nafcillin GC-MS (1 TMS) - 70eV, Positivesplash10-00di-9423600000-8e41142db1f7e5fa26c32017-10-06Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Nafcillin 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 - Nafcillin LC-ESI-QFT , negative-QTOFsplash10-00di-0090000000-65901bf6905f35a84f242017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Nafcillin LC-ESI-QFT , negative-QTOFsplash10-006x-0090000000-517308aedcbe6210d46e2017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Nafcillin LC-ESI-QFT , negative-QTOFsplash10-00dl-8390000000-c3d759b208856f69cc832017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Nafcillin LC-ESI-QFT , negative-QTOFsplash10-00di-9210000000-3431effabf1bb94e4b202017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Nafcillin LC-ESI-QFT , negative-QTOFsplash10-00di-9200000000-8d4bae5167cd78d8f0592017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Nafcillin LC-ESI-QFT , negative-QTOFsplash10-00di-9200000000-00cc24f858c63f2e6ac52017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Nafcillin LC-ESI-QFT , negative-QTOFsplash10-00di-9500000000-d447304de567843fa59a2017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Nafcillin LC-ESI-QFT , negative-QTOFsplash10-00xr-9500000000-fbdf096e0285a04fc3912017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Nafcillin LC-ESI-QFT , negative-QTOFsplash10-0600-9300000000-976ae9913f6b5bc3f2932017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Nafcillin LC-ESI-QFT , positive-QTOFsplash10-0002-0900000000-80966e1fb91b5e682c612017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Nafcillin LC-ESI-QFT , positive-QTOFsplash10-0002-0910000000-04c58a908553834f1db12017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Nafcillin LC-ESI-QFT , positive-QTOFsplash10-00dj-0900000000-9ab759b60ea1b1ccb0a72017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Nafcillin LC-ESI-QFT , positive-QTOFsplash10-00di-0900000000-1e9b29becf8d78e99cfa2017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Nafcillin LC-ESI-QFT , positive-QTOFsplash10-00xu-0900000000-dbba294d0a77e44851ed2017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Nafcillin LC-ESI-QFT , positive-QTOFsplash10-014i-0900000000-9ac2c1b4dcbf3f1421d92017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Nafcillin LC-ESI-QFT , positive-QTOFsplash10-014i-1900000000-46b494a78d0ebbbc80792017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Nafcillin LC-ESI-QFT , positive-QTOFsplash10-014i-7900000000-dc8fdcb9afe3b064db852017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Nafcillin LC-ESI-QFT , positive-QTOFsplash10-02ti-9300000000-847a94b299fb6ea1ddca2017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Nafcillin 15V, Negative-QTOFsplash10-00di-0090000000-c9457bba69de43e462e32021-09-20HMDB team, MONAView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Nafcillin 10V, Positive-QTOFsplash10-0900-0972300000-2fcf6e422525f18254132016-08-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Nafcillin 20V, Positive-QTOFsplash10-08fr-1950000000-56d3b44eb26e982069832016-08-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Nafcillin 40V, Positive-QTOFsplash10-08mi-2910000000-89a6a7cdc5521d4da9952016-08-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Nafcillin 10V, Negative-QTOFsplash10-00di-0091000000-e9e7c7093646248dfa762016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Nafcillin 20V, Negative-QTOFsplash10-00di-0293000000-58fe940779036ea827552016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Nafcillin 40V, Negative-QTOFsplash10-00bc-9751000000-54d52028a568bb18dd962016-08-03Wishart 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 DB00607 details
UrineExpected but not QuantifiedNot QuantifiedNot AvailableNot AvailableTaking drug identified by DrugBank entry DB00607 details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDDB00607
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID8634
KEGG Compound IDC07250
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNafcillin
METLIN IDNot Available
PubChem Compound8982
PDB IDNot Available
ChEBI ID7447
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 ReferencesNot Available

Enzymes

General function:
Involved in monooxygenase activity
Specific function:
Cytochromes P450 are a group of heme-thiolate monooxygenases. In liver microsomes, this enzyme is involved in an NADPH-dependent electron transport pathway. It performs a variety of oxidation reactions (e.g. caffeine 8-oxidation, omeprazole sulphoxidation, midazolam 1'-hydroxylation and midazolam 4-hydroxylation) of structurally unrelated compounds, including steroids, fatty acids, and xenobiotics. Acts as a 1,8-cineole 2-exo-monooxygenase. The enzyme also hydroxylates etoposide.
Gene Name:
CYP3A4
Uniprot ID:
P08684
Molecular weight:
57255.585
References
  1. Yasuda K, Ranade A, Venkataramanan R, Strom S, Chupka J, Ekins S, Schuetz E, Bachmann K: A comprehensive in vitro and in silico analysis of antibiotics that activate pregnane X receptor and induce CYP3A4 in liver and intestine. Drug Metab Dispos. 2008 Aug;36(8):1689-97. doi: 10.1124/dmd.108.020701. Epub 2008 May 27. [PubMed:18505790 ]
  2. Kim KY, Frey RJ, Epplen K, Foruhari F: Interaction between warfarin and nafcillin: case report and review of the literature. Pharmacotherapy. 2007 Oct;27(10):1467-70. [PubMed:17896903 ]
  3. Lang CC, Jamal SK, Mohamed Z, Mustafa MR, Mustafa AM, Lee TC: Evidence of an interaction between nifedipine and nafcillin in humans. Br J Clin Pharmacol. 2003 Jun;55(6):588-90. [PubMed:12814453 ]
General function:
Involved in monooxygenase activity
Specific function:
Cytochromes P450 are a group of heme-thiolate monooxygenases. In liver microsomes, this enzyme is involved in an NADPH-dependent electron transport pathway. It oxidizes a variety of structurally unrelated compounds, including steroids, fatty acids, and xenobiotics. Most active in catalyzing 2-hydroxylation. Caffeine is metabolized primarily by cytochrome CYP1A2 in the liver through an initial N3-demethylation. Also acts in the metabolism of aflatoxin B1 and acetaminophen. Participates in the bioactivation of carcinogenic aromatic and heterocyclic amines. Catalizes the N-hydroxylation of heterocyclic amines and the O-deethylation of phenacetin.
Gene Name:
CYP1A2
Uniprot ID:
P05177
Molecular weight:
58406.915

Transporters

General function:
Involved in ion transmembrane transporter activity
Specific function:
Involved in the renal elimination of endogenous and exogenous organic anions. Functions as organic anion exchanger when the uptake of one molecule of organic anion is coupled with an efflux of one molecule of endogenous dicarboxylic acid (glutarate, ketoglutarate, etc). Mediates the sodium-independent uptake of 2,3-dimercapto-1-propanesulfonic acid (DMPS). Mediates the sodium-independent uptake of p- aminohippurate (PAH), ochratoxin (OTA), acyclovir (ACV), 3'-azido- 3-'deoxythymidine (AZT), cimetidine (CMD), 2,4-dichloro- phenoxyacetate (2,4-D), hippurate (HA), indoleacetate (IA), indoxyl sulfate (IS) and 3-carboxy-4-methyl-5-propyl-2- furanpropionate (CMPF), cidofovir, adefovir, 9-(2- phosphonylmethoxyethyl) guanine (PMEG), 9-(2- phosphonylmethoxyethyl) diaminopurine (PMEDAP) and edaravone sulfate. PAH uptake is inhibited by p- chloromercuribenzenesulphonate (PCMBS), diethyl pyrocarbonate (DEPC), sulindac, diclofenac, carprofen, glutarate and okadaic acid. PAH uptake is inhibited by benzothiazolylcysteine (BTC), S-chlorotrifluoroethylcysteine (CTFC), cysteine S-conjugates S-dichlorovinylcysteine (DCVC), furosemide, steviol, phorbol 12-myristate 13-acetate (PMA), calcium ionophore A23187, benzylpenicillin, furosemide, indomethacin, bumetamide, losartan, probenecid, phenol red, urate, and alpha-ketoglutarate
Gene Name:
SLC22A6
Uniprot ID:
Q4U2R8
Molecular weight:
61815.8
References
  1. Jariyawat S, Sekine T, Takeda M, Apiwattanakul N, Kanai Y, Sophasan S, Endou H: The interaction and transport of beta-lactam antibiotics with the cloned rat renal organic anion transporter 1. J Pharmacol Exp Ther. 1999 Aug;290(2):672-7. [PubMed:10411577 ]