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Showing metabocard for N-Formylglycine (HMDB0255145)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-11 14:43:05 UTC
Update Date2021-09-26 23:09:43 UTC
HMDB IDHMDB0255145
Secondary Accession NumbersNone
Metabolite Identification
Common NameN-Formylglycine
DescriptionN-Formylglycine, also known as fgly or for-gly-OH, belongs to the class of organic compounds known as n-formyl-alpha amino acids. N-formyl-alpha amino acids are compounds containing an alpha amino acid which bears a formyl group at its terminal nitrogen atom. Based on a literature review a significant number of articles have been published on N-Formylglycine. This compound has been identified in human blood as reported by (PMID: 31557052 ). N-formylglycine is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically N-Formylglycine 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
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0255145 (N-Formylglycine)


  Mrv1652309112116432D          

  7  6  0  0  0  0            999 V2000
    1.2375    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5230    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1914    0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5230    1.9520    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9520    1.1270    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3809    1.1270    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  2  4  1  0  0  0  0
  1  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
M  END
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3D MOL for HMDB0255145 (N-Formylglycine)

HMDB0255145
     RDKit          3D
N-Formylglycine
 12 11  0  0  0  0  0  0  0  0999 V2000
    2.6755    0.3254    0.2448 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9532   -0.6101   -0.2642 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5738   -0.4990   -0.2627 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0376    0.7725    0.2602 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4399    0.5450    0.4085 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0163    0.6635    1.4595 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2925    0.1724   -0.6891 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3827   -1.5148   -0.6879 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0645   -1.2899   -0.6573 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4708    0.7872    1.2801 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2233    1.5539   -0.3765 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4287   -0.9062   -0.7154 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  2  0
  5  7  1  0
  2  8  1  0
  3  9  1  0
  4 10  1  0
  4 11  1  0
  7 12  1  0
M  END
Download

3D SDF for HMDB0255145 (N-Formylglycine)


  Mrv1652309112116432D          

  7  6  0  0  0  0            999 V2000
    1.2375    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5230    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1914    0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5230    1.9520    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9520    1.1270    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3809    1.1270    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  2  4  1  0  0  0  0
  1  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0255145

> <DATABASE_NAME>
hmdb

> <SMILES>
OC(=O)CNC=O

> <INCHI_IDENTIFIER>
InChI=1S/C3H5NO3/c5-2-4-1-3(6)7/h2H,1H2,(H,4,5)(H,6,7)

> <INCHI_KEY>
UGJBHEZMOKVTIM-UHFFFAOYSA-N

> <FORMULA>
C3H5NO3

> <MOLECULAR_WEIGHT>
103.077

> <EXACT_MASS>
103.026943025

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
12

> <JCHEM_AVERAGE_POLARIZABILITY>
8.67010223320467

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-formamidoacetic acid

> <ALOGPS_LOGP>
-1.49

> <JCHEM_LOGP>
-1.377327662

> <ALOGPS_LOGS>
-0.34

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
15.618853678345157

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.5595639113841373

> <JCHEM_PKA_STRONGEST_BASIC>
-1.5739708662794065

> <JCHEM_POLAR_SURFACE_AREA>
66.4

> <JCHEM_REFRACTIVITY>
20.9567

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.67e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
glycine, N-formyl-

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0255145 (N-Formylglycine)

HMDB0255145
     RDKit          3D
N-Formylglycine
 12 11  0  0  0  0  0  0  0  0999 V2000
    2.6755    0.3254    0.2448 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9532   -0.6101   -0.2642 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5738   -0.4990   -0.2627 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0376    0.7725    0.2602 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4399    0.5450    0.4085 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0163    0.6635    1.4595 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2925    0.1724   -0.6891 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3827   -1.5148   -0.6879 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0645   -1.2899   -0.6573 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4708    0.7872    1.2801 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2233    1.5539   -0.3765 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4287   -0.9062   -0.7154 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  2  0
  5  7  1  0
  2  8  1  0
  3  9  1  0
  4 10  1  0
  4 11  1  0
  7 12  1  0
M  END
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PDB for HMDB0255145 (N-Formylglycine)

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       2.310   1.334   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.976   2.104   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0      -0.357   1.334   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0       0.976   3.644   0.000  0.00  0.00           O+0
HETATM    5  N   UNK     0       3.644   2.104   0.000  0.00  0.00           N+0
HETATM    6  C   UNK     0       4.977   1.334   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       6.311   2.104   0.000  0.00  0.00           O+0
CONECT    1    2    5                                                       
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2                                                            
CONECT    5    1    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6                                                            
MASTER        0    0    0    0    0    0    0    0    7    0   12    0
END
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3D PDB for HMDB0255145 (N-Formylglycine)

COMPND    HMDB0255145
HETATM    1  O1  UNL     1       2.676   0.325   0.245  1.00  0.00           O  
HETATM    2  C1  UNL     1       1.953  -0.610  -0.264  1.00  0.00           C  
HETATM    3  N1  UNL     1       0.574  -0.499  -0.263  1.00  0.00           N  
HETATM    4  C2  UNL     1      -0.038   0.772   0.260  1.00  0.00           C  
HETATM    5  C3  UNL     1      -1.440   0.545   0.409  1.00  0.00           C  
HETATM    6  O2  UNL     1      -2.016   0.664   1.460  1.00  0.00           O  
HETATM    7  O3  UNL     1      -2.293   0.172  -0.689  1.00  0.00           O  
HETATM    8  H1  UNL     1       2.383  -1.515  -0.688  1.00  0.00           H  
HETATM    9  H2  UNL     1      -0.064  -1.290  -0.657  1.00  0.00           H  
HETATM   10  H3  UNL     1       0.471   0.787   1.280  1.00  0.00           H  
HETATM   11  H4  UNL     1       0.223   1.554  -0.376  1.00  0.00           H  
HETATM   12  H5  UNL     1      -2.429  -0.906  -0.715  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    8
CONECT    3    4    9
CONECT    4    5   10   11
CONECT    5    6    6    7
CONECT    7   12
END
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SMILES for HMDB0255145 (N-Formylglycine)

OC(=O)CNC=O
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INCHI for HMDB0255145 (N-Formylglycine)

InChI=1S/C3H5NO3/c5-2-4-1-3(6)7/h2H,1H2,(H,4,5)(H,6,7)
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
2-Formamidoacetic acidChEBI
FGlyChEBI
For-gly-OHChEBI
Formamidoacetic acidChEBI
Formyl-gly-OHChEBI
Formylaminoacetic acidChEBI
FormylglycineChEBI
2-FormamidoacetateGenerator
FormamidoacetateGenerator
FormylaminoacetateGenerator
Chemical FormulaC3H5NO3
Average Molecular Weight103.077
Monoisotopic Molecular Weight103.026943025
IUPAC Name2-formamidoacetic acid
Traditional Nameglycine, N-formyl-
CAS Registry NumberNot Available
SMILES
OC(=O)CNC=O
InChI Identifier
InChI=1S/C3H5NO3/c5-2-4-1-3(6)7/h2H,1H2,(H,4,5)(H,6,7)
InChI KeyUGJBHEZMOKVTIM-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as n-formyl-alpha amino acids. N-formyl-alpha amino acids are compounds containing an alpha amino acid which bears a formyl group at its terminal nitrogen atom.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassCarboxylic acids and derivatives
Sub ClassAmino acids, peptides, and analogues
Direct ParentN-formyl-alpha amino acids
Alternative Parents
Substituents
  • N-formyl-alpha-amino acid
  • Secondary carboxylic acid amide
  • Carboxamide group
  • Monocarboxylic acid or derivatives
  • Carboxylic acid
  • Organic nitrogen compound
  • Organic oxygen compound
  • Organopnictogen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organooxygen compound
  • Organonitrogen compound
  • Carbonyl group
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
ProcessNot Available
RoleNot Available
Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
logP-1.5ALOGPS
logP-1.4ChemAxon
logS-0.34ALOGPS
pKa (Strongest Acidic)3.56ChemAxon
pKa (Strongest Basic)-1.6ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area66.4 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity20.96 m³·mol⁻¹ChemAxon
Polarizability8.67 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DeepCCS[M+H]+121.09430932474
DeepCCS[M-H]-119.19930932474
DeepCCS[M-2H]-154.5930932474
DeepCCS[M+Na]+128.96630932474
AllCCS[M+H]+125.532859911
AllCCS[M+H-H2O]+121.332859911
AllCCS[M+NH4]+129.532859911
AllCCS[M+Na]+130.732859911
AllCCS[M-H]-121.732859911
AllCCS[M+Na-2H]-125.632859911
AllCCS[M+HCOO]-129.832859911

Predicted Retention Times

Underivatized

Chromatographic MethodRetention TimeReference
Predicted by Siyang on May 30, 20228.711 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20224.81 minutes32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid545.4 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid351.1 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid68.7 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid248.0 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid100.3 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid270.6 seconds40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid244.7 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)692.5 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid573.9 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid48.7 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid724.7 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid224.5 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid301.3 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate674.1 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA344.9 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water319.8 seconds40023050

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
N-FormylglycineOC(=O)CNC=O2017.3Standard polar33892256
N-FormylglycineOC(=O)CNC=O1063.7Standard non polar33892256
N-FormylglycineOC(=O)CNC=O1327.7Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
N-Formylglycine,2TMS,isomer #1C[Si](C)(C)OC(=O)CN(C=O)[Si](C)(C)C1371.6Semi standard non polar33892256
N-Formylglycine,2TMS,isomer #1C[Si](C)(C)OC(=O)CN(C=O)[Si](C)(C)C1290.0Standard non polar33892256
N-Formylglycine,2TMS,isomer #1C[Si](C)(C)OC(=O)CN(C=O)[Si](C)(C)C1462.1Standard polar33892256
N-Formylglycine,2TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC(=O)CN(C=O)[Si](C)(C)C(C)(C)C1741.9Semi standard non polar33892256
N-Formylglycine,2TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC(=O)CN(C=O)[Si](C)(C)C(C)(C)C1708.3Standard non polar33892256
N-Formylglycine,2TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC(=O)CN(C=O)[Si](C)(C)C(C)(C)C1727.0Standard polar33892256
Spectra
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID68130
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound75606
PDB IDNot Available
ChEBI ID21717
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. 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 ]