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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2017-03-23 01:46:49 UTC

Update Date

2019-07-23 07:18:35 UTC

HMDB ID

HMDB0062463

Secondary Accession Numbers

HMDB62463

Metabolite Identification

Common Name

chondroitin sulfate E (GalNAc4,6diS-GlcA), precursor 3

Description

chondroitin sulfate E (GalNAc4,6diS-GlcA) proteoglycan belongs to the class of organic compounds known as phenylpyrazoles. Phenylpyrazoles are compounds containing a phenylpyrazole skeleton, which consists of a pyrazole bound to a phenyl group. chondroitin sulfate E (GalNAc4,6diS-GlcA) proteoglycan is a strong basic compound (based on its pKa).

Structure

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

  Mrv1652303102017002D          

 14 15  0  0  0  0            999 V2000
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3819   -1.7224    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.1270   -2.5070    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.3020   -2.5070    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1830   -3.1745    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0470   -1.7224    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6119   -3.1745    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4324   -3.0882    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9173   -3.7557    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5817   -4.5094    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0667   -5.1768    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    1.7613   -4.5956    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2763   -3.9282    0.0000 C   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
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  5  7  2  0  0  0  0
  2  7  1  0  0  0  0
  4  8  1  0  0  0  0
  8  9  2  0  0  0  0
  9 10  1  0  0  0  0
 10 11  2  0  0  0  0
 11 12  1  0  0  0  0
 11 13  1  0  0  0  0
 13 14  2  0  0  0  0
  8 14  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0062463

> <DATABASE_NAME>
hmdb

> <SMILES>
CC1=NN(C(N)=C1)C1=CC=C(Cl)C=C1

> <INCHI_IDENTIFIER>
InChI=1S/C10H10ClN3/c1-7-6-10(12)14(13-7)9-4-2-8(11)3-5-9/h2-6H,12H2,1H3

> <INCHI_KEY>
CLORQKXFDBKDCZ-UHFFFAOYSA-N

> <FORMULA>
C10H10ClN3

> <MOLECULAR_WEIGHT>
207.66

> <EXACT_MASS>
207.056325

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
24

> <JCHEM_AVERAGE_POLARIZABILITY>
21.6159874346577

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
1-(4-chlorophenyl)-3-methyl-1H-pyrazol-5-amine

> <ALOGPS_LOGP>
2.63

> <JCHEM_LOGP>
2.054844222333333

> <ALOGPS_LOGS>
-2.40

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
4.439743174775669

> <JCHEM_POLAR_SURFACE_AREA>
43.84

> <JCHEM_REFRACTIVITY>
57.769700000000014

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
8.26e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-(4-chlorophenyl)-5-methylpyrazol-3-amine

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 10-MAR-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   10-MAR-20         0                                  
HETATM    1  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    3  N   UNK     0       2.580  -3.215   0.000  0.00  0.00           N+0
HETATM    4  N   UNK     0       2.104  -4.680   0.000  0.00  0.00           N+0
HETATM    5  C   UNK     0       0.564  -4.680   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0      -0.342  -5.926   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0       0.088  -3.215   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       3.009  -5.926   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       4.540  -5.765   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       5.446  -7.011   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       4.819  -8.418   0.000  0.00  0.00           C+0
HETATM   12 Cl   UNK     0       5.725  -9.663   0.000  0.00  0.00          Cl+0
HETATM   13  C   UNK     0       3.288  -8.578   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       2.382  -7.333   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3    7                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5    8                                                  
CONECT    5    4    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5    2                                                       
CONECT    8    4    9   14                                                  
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11   14                                                       
CONECT   14   13    8                                                       
MASTER        0    0    0    0    0    0    0    0   14    0   30    0
END

View in JSmol View Stereo Labels

Synonyms

Value	Source
Chondroitin sulfuric acid e (galnac4,6Dis-glca) proteoglycan	Generator
Chondroitin sulphate e (galnac4,6Dis-glca) proteoglycan	Generator
Chondroitin sulphuric acid e (galnac4,6Dis-glca) proteoglycan	Generator

Chemical Formula

C₁₀H₁₀ClN₃

Average Molecular Weight

207.66

Monoisotopic Molecular Weight

207.056325

IUPAC Name

1-(4-chlorophenyl)-3-methyl-1H-pyrazol-5-amine

Traditional Name

2-(4-chlorophenyl)-5-methylpyrazol-3-amine

CAS Registry Number

Not Available

SMILES

CC1=NN(C(N)=C1)C1=CC=C(Cl)C=C1

InChI Identifier

InChI=1S/C10H10ClN3/c1-7-6-10(12)14(13-7)9-4-2-8(11)3-5-9/h2-6H,12H2,1H3

InChI Key

CLORQKXFDBKDCZ-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as phenylpyrazoles. Phenylpyrazoles are compounds containing a phenylpyrazole skeleton, which consists of a pyrazole bound to a phenyl group.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Azoles

Sub Class

Pyrazoles

Direct Parent

Phenylpyrazoles

Alternative Parents

Substituents

Phenylpyrazole
Chlorobenzene
Halobenzene
Aryl chloride
Aryl halide
Monocyclic benzene moiety
Benzenoid
Heteroaromatic compound
Azacycle
Organochloride
Organohalogen compound
Primary amine
Amine
Hydrocarbon derivative
Organopnictogen compound
Organic nitrogen compound
Organonitrogen compound
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

Not Available

Ontology

Not Available

Endogenous (HMDB: HMDB0062463)

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	0.83 g/l	ALOGPS
LogP	2.63	ALOGPS

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
logP	2.63	ALOGPS
logP	2.05	ChemAxon
logS	-2.4	ALOGPS
pKa (Strongest Basic)	4.44	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	2	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	43.84 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	57.77 m³·mol⁻¹	ChemAxon
Polarizability	21.62 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]+	146.067	30932474
DeepCCS	[M-H]-	143.671	30932474
DeepCCS	[M-2H]-	177.313	30932474
DeepCCS	[M+Na]+	152.038	30932474
AllCCS	[M+H]+	144.5	32859911
AllCCS	[M+H-H2O]+	140.3	32859911
AllCCS	[M+NH4]+	148.4	32859911
AllCCS	[M+Na]+	149.5	32859911
AllCCS	[M-H]-	144.0	32859911
AllCCS	[M+Na-2H]-	144.3	32859911
AllCCS	[M+HCOO]-	144.7	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
chondroitin sulfate E (GalNAc4,6diS-GlcA), precursor 3	CC1=NN(C(N)=C1)C1=CC=C(Cl)C=C1	2906.0	Standard polar	33892256
chondroitin sulfate E (GalNAc4,6diS-GlcA), precursor 3	CC1=NN(C(N)=C1)C1=CC=C(Cl)C=C1	1848.2	Standard non polar	33892256
chondroitin sulfate E (GalNAc4,6diS-GlcA), precursor 3	CC1=NN(C(N)=C1)C1=CC=C(Cl)C=C1	1895.4	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
chondroitin sulfate E (GalNAc4,6diS-GlcA), precursor 3,1TMS,isomer #1	CC1=NN(C2=CC=C(Cl)C=C2)C(N[Si](C)(C)C)=C1	1993.7	Semi standard non polar	33892256
chondroitin sulfate E (GalNAc4,6diS-GlcA), precursor 3,1TMS,isomer #1	CC1=NN(C2=CC=C(Cl)C=C2)C(N[Si](C)(C)C)=C1	1999.4	Standard non polar	33892256
chondroitin sulfate E (GalNAc4,6diS-GlcA), precursor 3,1TMS,isomer #1	CC1=NN(C2=CC=C(Cl)C=C2)C(N[Si](C)(C)C)=C1	2629.9	Standard polar	33892256
chondroitin sulfate E (GalNAc4,6diS-GlcA), precursor 3,2TMS,isomer #1	CC1=NN(C2=CC=C(Cl)C=C2)C(N([Si](C)(C)C)[Si](C)(C)C)=C1	1896.6	Semi standard non polar	33892256
chondroitin sulfate E (GalNAc4,6diS-GlcA), precursor 3,2TMS,isomer #1	CC1=NN(C2=CC=C(Cl)C=C2)C(N([Si](C)(C)C)[Si](C)(C)C)=C1	2128.0	Standard non polar	33892256
chondroitin sulfate E (GalNAc4,6diS-GlcA), precursor 3,2TMS,isomer #1	CC1=NN(C2=CC=C(Cl)C=C2)C(N([Si](C)(C)C)[Si](C)(C)C)=C1	2389.5	Standard polar	33892256
chondroitin sulfate E (GalNAc4,6diS-GlcA), precursor 3,1TBDMS,isomer #1	CC1=NN(C2=CC=C(Cl)C=C2)C(N[Si](C)(C)C(C)(C)C)=C1	2172.5	Semi standard non polar	33892256
chondroitin sulfate E (GalNAc4,6diS-GlcA), precursor 3,1TBDMS,isomer #1	CC1=NN(C2=CC=C(Cl)C=C2)C(N[Si](C)(C)C(C)(C)C)=C1	2212.1	Standard non polar	33892256
chondroitin sulfate E (GalNAc4,6diS-GlcA), precursor 3,1TBDMS,isomer #1	CC1=NN(C2=CC=C(Cl)C=C2)C(N[Si](C)(C)C(C)(C)C)=C1	2715.5	Standard polar	33892256
chondroitin sulfate E (GalNAc4,6diS-GlcA), precursor 3,2TBDMS,isomer #1	CC1=NN(C2=CC=C(Cl)C=C2)C(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=C1	2368.5	Semi standard non polar	33892256
chondroitin sulfate E (GalNAc4,6diS-GlcA), precursor 3,2TBDMS,isomer #1	CC1=NN(C2=CC=C(Cl)C=C2)C(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=C1	2507.7	Standard non polar	33892256
chondroitin sulfate E (GalNAc4,6diS-GlcA), precursor 3,2TBDMS,isomer #1	CC1=NN(C2=CC=C(Cl)C=C2)C(N([Si](C)(C)C(C)(C)C)[Si](C)(C)C(C)(C)C)=C1	2541.4	Standard polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - chondroitin sulfate E (GalNAc4,6diS-GlcA), precursor 3 GC-MS (Non-derivatized) - 70eV, Positive	splash10-0a4i-6960000000-418e10465532dc369f7d	2017-09-20	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - chondroitin sulfate E (GalNAc4,6diS-GlcA), precursor 3 GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - chondroitin sulfate E (GalNAc4,6diS-GlcA), precursor 3 GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - chondroitin sulfate E (GalNAc4,6diS-GlcA), precursor 3 10V, Positive-QTOF	splash10-0a4i-0190000000-0121f29a5ed356cfd145	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - chondroitin sulfate E (GalNAc4,6diS-GlcA), precursor 3 20V, Positive-QTOF	splash10-0a4i-0390000000-a86252a101b231a4f093	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - chondroitin sulfate E (GalNAc4,6diS-GlcA), precursor 3 40V, Positive-QTOF	splash10-052o-9400000000-66258c0f3baa41bdd9fe	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - chondroitin sulfate E (GalNAc4,6diS-GlcA), precursor 3 10V, Negative-QTOF	splash10-0a4i-0090000000-421ae72be21d2f2e8656	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - chondroitin sulfate E (GalNAc4,6diS-GlcA), precursor 3 20V, Negative-QTOF	splash10-0a4i-1090000000-4d12f646cda6090ec705	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - chondroitin sulfate E (GalNAc4,6diS-GlcA), precursor 3 40V, Negative-QTOF	splash10-002f-9310000000-acdd7ae72253cb59dfee	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - chondroitin sulfate E (GalNAc4,6diS-GlcA), precursor 3 10V, Positive-QTOF	splash10-0a4i-0090000000-6f69e840c42b4cc6f368	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - chondroitin sulfate E (GalNAc4,6diS-GlcA), precursor 3 20V, Positive-QTOF	splash10-0a4i-0190000000-8be8475f82ed5cf7a6d2	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - chondroitin sulfate E (GalNAc4,6diS-GlcA), precursor 3 40V, Positive-QTOF	splash10-0ikl-4900000000-6c96b7ac9907ae9b5ced	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - chondroitin sulfate E (GalNAc4,6diS-GlcA), precursor 3 10V, Negative-QTOF	splash10-0a4i-0090000000-42c1c8759d7f28ffef4c	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - chondroitin sulfate E (GalNAc4,6diS-GlcA), precursor 3 20V, Negative-QTOF	splash10-0a4i-0190000000-331b40280ed3953279b4	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - chondroitin sulfate E (GalNAc4,6diS-GlcA), precursor 3 40V, Negative-QTOF	splash10-001i-9300000000-6bc842e40619135823a9	2021-09-22	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Not Available

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

FDB034838

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

170301

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

Not Available

Showing metabocard for chondroitin sulfate E (GalNAc4,6diS-GlcA), precursor 3 (HMDB0062463)

MOL for HMDB0062463 (chondroitin sulfate E (GalNAc4,6diS-GlcA), precursor 3)

3D MOL for HMDB0062463 (chondroitin sulfate E (GalNAc4,6diS-GlcA), precursor 3)

3D SDF for HMDB0062463 (chondroitin sulfate E (GalNAc4,6diS-GlcA), precursor 3)

3D-SDF for HMDB0062463 (chondroitin sulfate E (GalNAc4,6diS-GlcA), precursor 3)

PDB for HMDB0062463 (chondroitin sulfate E (GalNAc4,6diS-GlcA), precursor 3)

3D PDB for HMDB0062463 (chondroitin sulfate E (GalNAc4,6diS-GlcA), precursor 3)

SMILES for HMDB0062463 (chondroitin sulfate E (GalNAc4,6diS-GlcA), precursor 3)

INCHI for HMDB0062463 (chondroitin sulfate E (GalNAc4,6diS-GlcA), precursor 3)

Structure for HMDB0062463 (chondroitin sulfate E (GalNAc4,6diS-GlcA), precursor 3)

3D Structure for HMDB0062463 (chondroitin sulfate E (GalNAc4,6diS-GlcA), precursor 3)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra