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Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2021-09-11 14:44:13 UTC

Update Date

2021-09-26 23:09:45 UTC

HMDB ID

HMDB0255160

Secondary Accession Numbers

None

Metabolite Identification

Common Name

N-Hydroxysuccinimidyl-4-azidobenzoate

Description

N-Hydroxysuccinimidyl-4-azidobenzoate, also known as 4-azidobenzoyloxysuccinimide or HSAB, belongs to the class of organic compounds known as benzoic acids and derivatives. These are organic compounds containing a carboxylic acid substituent attached to a benzene ring. Based on a literature review a significant number of articles have been published on N-Hydroxysuccinimidyl-4-azidobenzoate. This compound has been identified in human blood as reported by (PMID: 31557052 ). N-hydroxysuccinimidyl-4-azidobenzoate is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically N-Hydroxysuccinimidyl-4-azidobenzoate 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


  Mrv1652309112116442D          

 19 20  0  0  0  0            999 V2000
    2.0964   -2.9599    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8414   -3.7445    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0164   -3.7445    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5315   -4.4120    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7615   -2.9599    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0231   -2.7050    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6362   -3.2570    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4647   -4.0640    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4208   -3.0021    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0339   -3.5541    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8186   -3.2992    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9901   -2.4922    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3770   -1.9402    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5924   -2.1951    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7747   -2.2373    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3878   -2.7893    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
   -5.0009   -3.3413    0.0000 N   0  5  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  3  5  1  0  0  0  0
  5  6  1  0  0  0  0
  1  6  1  0  0  0  0
  6  7  2  0  0  0  0
  5  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
  9 11  1  0  0  0  0
 11 12  2  0  0  0  0
 12 13  1  0  0  0  0
 13 14  2  0  0  0  0
 14 15  1  0  0  0  0
 15 16  2  0  0  0  0
 11 16  1  0  0  0  0
 14 17  1  0  0  0  0
 17 18  2  0  0  0  0
 18 19  2  0  0  0  0
M  CHG  2  18   1  19  -1
M  END
> <DATABASE_ID>
HMDB0255160

> <DATABASE_NAME>
hmdb

> <SMILES>
[N-]=[N+]=NC1=CC=C(C=C1)C(=O)ON1C(=O)CCC1=O

> <INCHI_IDENTIFIER>
InChI=1S/C11H8N4O4/c12-14-13-8-3-1-7(2-4-8)11(18)19-15-9(16)5-6-10(15)17/h1-4H,5-6H2

> <INCHI_KEY>
LWAVGNJLLQSNNN-UHFFFAOYSA-N

> <FORMULA>
C11H8N4O4

> <MOLECULAR_WEIGHT>
260.209

> <EXACT_MASS>
260.054554754

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
27

> <JCHEM_AVERAGE_POLARIZABILITY>
23.731745701377566

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
2,5-dioxopyrrolidin-1-yl 4-azidobenzoate

> <ALOGPS_LOGP>
2.00

> <JCHEM_LOGP>
1.6207836896666667

> <ALOGPS_LOGS>
-2.70

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
17.697299831475807

> <JCHEM_PKA_STRONGEST_BASIC>
-7.224900594079539

> <JCHEM_POLAR_SURFACE_AREA>
93.10999999999999

> <JCHEM_REFRACTIVITY>
64.1556

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.20e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2,5-dioxopyrrolidin-1-yl 4-azidobenzoate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 11-SEP-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   11-SEP-21         0                                  
HETATM    1  C   UNK     0       3.913  -5.525   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       3.437  -6.990   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.897  -6.990   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       0.992  -8.236   0.000  0.00  0.00           O+0
HETATM    5  N   UNK     0       1.421  -5.525   0.000  0.00  0.00           N+0
HETATM    6  C   UNK     0       2.667  -4.620   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       2.667  -3.080   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0      -0.043  -5.049   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0      -1.188  -6.080   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      -0.867  -7.586   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0      -2.652  -5.604   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -3.797  -6.634   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -5.261  -6.158   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -5.581  -4.652   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -4.437  -3.622   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      -2.972  -4.098   0.000  0.00  0.00           C+0
HETATM   17  N   UNK     0      -7.046  -4.176   0.000  0.00  0.00           N+0
HETATM   18  N   UNK     0      -8.191  -5.207   0.000  0.00  0.00           N+1
HETATM   19  N   UNK     0      -9.335  -6.237   0.000  0.00  0.00           N-1
CONECT    1    2    6                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6    8                                                  
CONECT    6    5    1    7                                                  
CONECT    7    6                                                            
CONECT    8    5    9                                                       
CONECT    9    8   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9   12   16                                                  
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15   17                                                  
CONECT   15   14   16                                                       
CONECT   16   15   11                                                       
CONECT   17   14   18                                                       
CONECT   18   17   19                                                       
CONECT   19   18                                                            
MASTER        0    0    0    0    0    0    0    0   19    0   40    0
END

COMPND    HMDB0255160
HETATM    1  N1  UNL     1       6.507  -1.637  -0.752  1.00  0.00           N1-
HETATM    2  N2  UNL     1       6.115  -0.525  -0.325  1.00  0.00           N1+
HETATM    3  N3  UNL     1       5.498   0.367   0.309  1.00  0.00           N  
HETATM    4  C1  UNL     1       4.085   0.427   0.182  1.00  0.00           C  
HETATM    5  C2  UNL     1       3.466   1.534  -0.345  1.00  0.00           C  
HETATM    6  C3  UNL     1       2.105   1.595  -0.463  1.00  0.00           C  
HETATM    7  C4  UNL     1       1.332   0.520  -0.042  1.00  0.00           C  
HETATM    8  C5  UNL     1      -0.122   0.548  -0.179  1.00  0.00           C  
HETATM    9  O1  UNL     1      -0.610   1.578  -0.741  1.00  0.00           O  
HETATM   10  O2  UNL     1      -0.981  -0.409   0.235  1.00  0.00           O  
HETATM   11  N4  UNL     1      -2.317  -0.451   0.152  1.00  0.00           N  
HETATM   12  C6  UNL     1      -3.133  -1.423   0.821  1.00  0.00           C  
HETATM   13  O3  UNL     1      -2.799  -2.447   1.479  1.00  0.00           O  
HETATM   14  C7  UNL     1      -4.585  -1.062   0.637  1.00  0.00           C  
HETATM   15  C8  UNL     1      -4.534   0.368   0.146  1.00  0.00           C  
HETATM   16  C9  UNL     1      -3.196   0.372  -0.556  1.00  0.00           C  
HETATM   17  O4  UNL     1      -2.966   1.016  -1.589  1.00  0.00           O  
HETATM   18  C10 UNL     1       1.962  -0.561   0.475  1.00  0.00           C  
HETATM   19  C11 UNL     1       3.332  -0.629   0.597  1.00  0.00           C  
HETATM   20  H1  UNL     1       4.039   2.407  -0.688  1.00  0.00           H  
HETATM   21  H2  UNL     1       1.591   2.469  -0.882  1.00  0.00           H  
HETATM   22  H3  UNL     1      -5.143  -1.072   1.591  1.00  0.00           H  
HETATM   23  H4  UNL     1      -5.052  -1.744  -0.072  1.00  0.00           H  
HETATM   24  H5  UNL     1      -4.450   1.076   0.996  1.00  0.00           H  
HETATM   25  H6  UNL     1      -5.353   0.598  -0.534  1.00  0.00           H  
HETATM   26  H7  UNL     1       1.364  -1.420   0.808  1.00  0.00           H  
HETATM   27  H8  UNL     1       3.846  -1.494   1.015  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    3
CONECT    3    4
CONECT    4    5    5   19
CONECT    5    6   20
CONECT    6    7    7   21
CONECT    7    8   18
CONECT    8    9    9   10
CONECT   10   11
CONECT   11   12   16
CONECT   12   13   13   14
CONECT   14   15   22   23
CONECT   15   16   24   25
CONECT   16   17   17
CONECT   18   19   19   26
CONECT   19   27
END

View in JSmol View Stereo Labels

Synonyms

Value	Source
N-Hydroxysuccinimidyl-4-azidobenzoic acid	Generator
4-Azidobenzoic acid N-hydroxysuccinimide ester	HMDB
4-Azidobenzoyloxysuccinimide	HMDB
HSAB	HMDB
Hydroxysuccinimidyl-4-azidobenzoate	HMDB
Hydroxysuccinimidyl-p-azidobenzoate	HMDB

Chemical Formula

C₁₁H₈N₄O₄

Average Molecular Weight

260.209

Monoisotopic Molecular Weight

260.054554754

IUPAC Name

2,5-dioxopyrrolidin-1-yl 4-azidobenzoate

Traditional Name

2,5-dioxopyrrolidin-1-yl 4-azidobenzoate

CAS Registry Number

Not Available

SMILES

[N-]=[N+]=NC1=CC=C(C=C1)C(=O)ON1C(=O)CCC1=O

InChI Identifier

InChI=1S/C11H8N4O4/c12-14-13-8-3-1-7(2-4-8)11(18)19-15-9(16)5-6-10(15)17/h1-4H,5-6H2

InChI Key

LWAVGNJLLQSNNN-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as benzoic acids and derivatives. These are organic compounds containing a carboxylic acid substituent attached to a benzene ring.

Kingdom

Organic compounds

Super Class

Benzenoids

Class

Benzene and substituted derivatives

Sub Class

Benzoic acids and derivatives

Direct Parent

Benzoic acids and derivatives

Alternative Parents

Substituents

Benzoic acid or derivatives
Benzoyl
Phenylazide
2-pyrrolidone
Pyrrolidone
Dicarboximide
Pyrrolidine
Azo compound
Azo imide
Carboxylic acid salt
Lactam
Carboxylic acid derivative
Azacycle
Organoheterocyclic compound
Monocarboxylic acid or derivatives
Organopnictogen compound
Organic oxygen compound
Organic nitrogen compound
Hydrocarbon derivative
Carbonyl group
Organic oxide
Organonitrogen compound
Organooxygen compound
Organic salt
Organic zwitterion
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

Not Available

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	2	ALOGPS
logP	1.62	ChemAxon
logS	-2.7	ALOGPS
pKa (Strongest Acidic)	17.7	ChemAxon
pKa (Strongest Basic)	-7.2	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	93.11 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	64.16 m³·mol⁻¹	ChemAxon
Polarizability	23.73 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	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]+	151.22	30932474
DeepCCS	[M-H]-	148.852	30932474
DeepCCS	[M-2H]-	182.165	30932474
DeepCCS	[M+Na]+	157.133	30932474
AllCCS	[M+H]+	156.1	32859911
AllCCS	[M+H-H2O]+	152.4	32859911
AllCCS	[M+NH4]+	159.5	32859911
AllCCS	[M+Na]+	160.5	32859911
AllCCS	[M-H]-	157.0	32859911
AllCCS	[M+Na-2H]-	156.6	32859911
AllCCS	[M+HCOO]-	156.2	32859911

Predicted Retention Times

Underivatized

Chromatographic Method	Retention Time	Reference
Predicted by Siyang on May 30, 2022	12.3885 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	2.57 minutes	32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	2092.6 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	352.9 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	129.7 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	204.9 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	115.8 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	404.5 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	577.1 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	89.2 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	981.0 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	375.1 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	1315.8 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	301.5 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	364.9 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	436.4 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	251.5 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	138.7 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
N-Hydroxysuccinimidyl-4-azidobenzoate	[N-]=[N+]=NC1=CC=C(C=C1)C(=O)ON1C(=O)CCC1=O	3581.0	Standard polar	33892256
N-Hydroxysuccinimidyl-4-azidobenzoate	[N-]=[N+]=NC1=CC=C(C=C1)C(=O)ON1C(=O)CCC1=O	2450.5	Standard non polar	33892256
N-Hydroxysuccinimidyl-4-azidobenzoate	[N-]=[N+]=NC1=CC=C(C=C1)C(=O)ON1C(=O)CCC1=O	2352.6	Semi standard non polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - N-Hydroxysuccinimidyl-4-azidobenzoate GC-MS (Non-derivatized) - 70eV, Positive	splash10-002b-9610000000-b7fd55b96aea10c25057	2021-09-24	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - N-Hydroxysuccinimidyl-4-azidobenzoate GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	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

108951

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

122153

PDB ID

Not Available

ChEBI ID

Not Available

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 N-Hydroxysuccinimidyl-4-azidobenzoate (HMDB0255160)

MOL for HMDB0255160 (N-Hydroxysuccinimidyl-4-azidobenzoate)

3D MOL for HMDB0255160 (N-Hydroxysuccinimidyl-4-azidobenzoate)

3D SDF for HMDB0255160 (N-Hydroxysuccinimidyl-4-azidobenzoate)

3D-SDF for HMDB0255160 (N-Hydroxysuccinimidyl-4-azidobenzoate)

PDB for HMDB0255160 (N-Hydroxysuccinimidyl-4-azidobenzoate)

3D PDB for HMDB0255160 (N-Hydroxysuccinimidyl-4-azidobenzoate)

SMILES for HMDB0255160 (N-Hydroxysuccinimidyl-4-azidobenzoate)

INCHI for HMDB0255160 (N-Hydroxysuccinimidyl-4-azidobenzoate)

Structure for HMDB0255160 (N-Hydroxysuccinimidyl-4-azidobenzoate)

3D Structure for HMDB0255160 (N-Hydroxysuccinimidyl-4-azidobenzoate)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

GC-MS Spectra