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Identification Taxonomy Ontology Physical properties Spectra Biological properties Concentrations Links References XML

Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2021-09-11 14:00:58 UTC

Update Date

2021-09-26 23:08:45 UTC

HMDB ID

HMDB0254633

Secondary Accession Numbers

None

Metabolite Identification

Common Name

Medina

Description

Medina belongs to the class of organic compounds known as nitramines. These are organyl derivatives of nitramide with the general formula RNHO2 (R = organyl group). Based on a literature review a significant number of articles have been published on Medina. This compound has been identified in human blood as reported by (PMID: 31557052 ). Medina is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Medina is part of the human exposome. The exposome can be defined as the collection of all the exposures of an individual in a lifetime and how those exposures relate to health. An individual's exposure begins before birth and includes insults from environmental and occupational sources.

Structure

MOL 3D MOL SDF 3D SDF PDB 3D PDB SMILES InChI

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	Source
Methylene dinitramine	ChEBI
MEDINA	ChEBI

Chemical Formula

CH₄N₄O₄

Average Molecular Weight

136.067

Monoisotopic Molecular Weight

136.023254625

IUPAC Name

nitro[(nitroamino)methyl]amine

Traditional Name

methylenedinitramine

CAS Registry Number

Not Available

SMILES

[O-][N+](=O)NCN[N+]([O-])=O

InChI Identifier

InChI=1S/CH4N4O4/c6-4(7)2-1-3-5(8)9/h2-3H,1H2

InChI Key

HSMJRIUFXFAZSY-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as nitramines. These are organyl derivatives of nitramide with the general formula RNHO2 (R = organyl group).

Kingdom

Organic compounds

Super Class

Organic 1,3-dipolar compounds

Class

Allyl-type 1,3-dipolar organic compounds

Sub Class

Organic nitro compounds

Direct Parent

Nitramines

Alternative Parents

Substituents

Nitramine
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Organonitrogen compound
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

one-carbon compound (CHEBI:25296 )
nitramine (CHEBI:25296 )

Ontology

Physiological effect

Not Available

Disposition

Biological location

Non-excretory biofluid

Biofluid or Excreta

Blood (PMID: 31557052)

Source

Exogenous

Exogenous (PMID: 31557052)

Process

Not Available

Role

Not Available

Physical Properties

State

Not Available

Experimental Molecular Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
logP	-0.18	ALOGPS
logP	-3.9	ChemAxon
logS	-2.2	ALOGPS
pKa (Strongest Acidic)	9.18	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	110.34 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	24.64 m³·mol⁻¹	ChemAxon
Polarizability	9.42 Å³	ChemAxon
Number of Rings	0	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DeepCCS	[M+H]+	118.042	30932474
DeepCCS	[M-H]-	114.82	30932474
DeepCCS	[M-2H]-	152.242	30932474
DeepCCS	[M+Na]+	126.988	30932474
AllCCS	[M+H]+	132.2	32859911
AllCCS	[M+H-H2O]+	128.2	32859911
AllCCS	[M+NH4]+	135.9	32859911
AllCCS	[M+Na]+	137.0	32859911
AllCCS	[M-H]-	124.1	32859911
AllCCS	[M+Na-2H]-	126.9	32859911
AllCCS	[M+HCOO]-	129.9	32859911

Predicted Retention Times

Underivatized

Chromatographic Method	Retention Time	Reference
Predicted by Siyang on May 30, 2022	11.7974 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	2.71 minutes	32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	937.2 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	415.0 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	87.7 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	295.0 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	88.7 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	301.2 seconds	40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid	472.2 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	456.9 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	723.5 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	105.8 seconds	40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid	930.7 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	259.1 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	273.3 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	806.5 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	324.2 seconds	40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water	368.7 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Medina	[O-][N+](=O)NCN[N+]([O-])=O	2438.4	Standard polar	33892256
Medina	[O-][N+](=O)NCN[N+]([O-])=O	1664.7	Standard non polar	33892256
Medina	[O-][N+](=O)NCN[N+]([O-])=O	1353.0	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Medina,1TMS,isomer #1	C[Si](C)(C)N(CN[N+](=O)[O-])[N+](=O)[O-]	1539.5	Semi standard non polar	33892256
Medina,1TMS,isomer #1	C[Si](C)(C)N(CN[N+](=O)[O-])[N+](=O)[O-]	1449.2	Standard non polar	33892256
Medina,1TMS,isomer #1	C[Si](C)(C)N(CN[N+](=O)[O-])[N+](=O)[O-]	2161.9	Standard polar	33892256
Medina,2TMS,isomer #1	C[Si](C)(C)N(CN([N+](=O)[O-])[Si](C)(C)C)[N+](=O)[O-]	1506.7	Semi standard non polar	33892256
Medina,2TMS,isomer #1	C[Si](C)(C)N(CN([N+](=O)[O-])[Si](C)(C)C)[N+](=O)[O-]	1624.7	Standard non polar	33892256
Medina,2TMS,isomer #1	C[Si](C)(C)N(CN([N+](=O)[O-])[Si](C)(C)C)[N+](=O)[O-]	1955.8	Standard polar	33892256
Medina,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)N(CN[N+](=O)[O-])[N+](=O)[O-]	1766.8	Semi standard non polar	33892256
Medina,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)N(CN[N+](=O)[O-])[N+](=O)[O-]	1628.3	Standard non polar	33892256
Medina,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)N(CN[N+](=O)[O-])[N+](=O)[O-]	2150.8	Standard polar	33892256
Medina,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)N(CN([N+](=O)[O-])[Si](C)(C)C(C)(C)C)[N+](=O)[O-]	1966.9	Semi standard non polar	33892256
Medina,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)N(CN([N+](=O)[O-])[Si](C)(C)C(C)(C)C)[N+](=O)[O-]	1997.5	Standard non polar	33892256
Medina,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)N(CN([N+](=O)[O-])[Si](C)(C)C(C)(C)C)[N+](=O)[O-]	2066.0	Standard polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - Medina GC-MS (Non-derivatized) - 70eV, Positive	splash10-004i-9000000000-29ff5150f1979e085f62	2021-09-24	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Medina GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-10-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-10-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-10-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-10-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-10-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-10-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-10-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-10-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-10-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-10-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-10-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-10-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-10-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-10-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-10-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-10-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-10-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-10-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-10-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-10-25	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Blood

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	31557052	details

Abnormal Concentrations

Not Available

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

24707

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Medina

METLIN ID

Not Available

PubChem Compound

26524

PDB ID

Not Available

ChEBI ID

25296

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

Barupal DK, Fiehn O: Generating the Blood Exposome Database Using a Comprehensive Text Mining and Database Fusion Approach. Environ Health Perspect. 2019 Sep;127(9):97008. doi: 10.1289/EHP4713. Epub 2019 Sep 26. [PubMed:31557052 ]

Showing metabocard for Medina (HMDB0254633)

MOL for HMDB0254633 (Medina)

3D MOL for HMDB0254633 (Medina)

3D SDF for HMDB0254633 (Medina)

3D-SDF for HMDB0254633 (Medina)

PDB for HMDB0254633 (Medina)

3D PDB for HMDB0254633 (Medina)

SMILES for HMDB0254633 (Medina)

INCHI for HMDB0254633 (Medina)

Structure for HMDB0254633 (Medina)

3D Structure for HMDB0254633 (Medina)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

NMR Spectra