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Showing metabocard for 6-Isothiocyanato-1-hexene (HMDB0038436)

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IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesXML
Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-09-11 23:45:13 UTC
Update Date2023-02-21 17:26:34 UTC
HMDB IDHMDB0038436
Secondary Accession Numbers
  • HMDB38436
Metabolite Identification
Common Name6-Isothiocyanato-1-hexene
Description6-Isothiocyanato-1-hexene belongs to the class of organic compounds known as isothiocyanates. These are organic compounds containing the isothiocyanate group, an isocyanate analogue with the general formula RN=C=S. 6-Isothiocyanato-1-hexene has been detected, but not quantified in, brassicas and root vegetables. This could make 6-isothiocyanato-1-hexene a potential biomarker for the consumption of these foods. Based on a literature review very few articles have been published on 6-Isothiocyanato-1-hexene.
Structure
Data?1677000394
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0038436 (6-Isothiocyanato-1-hexene)


  Mrv0541 05061310272D          

  9  8  0  0  0  0            999 V2000
    1.7605    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1895    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9039    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6184    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3329    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.7618    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0474    1.8414    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    7.4763    1.0164    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  2  0  0  0  0
  3  2  1  0  0  0  0
  4  3  1  0  0  0  0
  5  4  1  0  0  0  0
  6  5  1  0  0  0  0
  8  6  1  0  0  0  0
  8  7  2  0  0  0  0
  9  7  2  0  0  0  0
M  END
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3D MOL for HMDB0038436 (6-Isothiocyanato-1-hexene)

HMDB0038436
     RDKit          3D
6-Isothiocyanato-1-hexene
 20 19  0  0  0  0  0  0  0  0999 V2000
   -2.8216    1.4489   -0.1678 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6488    0.9956   -0.6017 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4760   -0.4160   -1.0118 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4461   -1.1096   -0.1579 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8546   -0.4176   -0.2992 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9742   -1.0264    0.5034 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1632   -0.2331    0.2508 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.1344    0.9773    0.6757 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4685    2.5134    1.0327 S   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9034    2.4808    0.1199 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6431    0.7536   -0.1247 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7909    1.6545   -0.6690 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1570   -0.3855   -2.0906 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4407   -0.9656   -1.0262 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7915   -1.2561    0.8728 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3304   -2.1506   -0.5772 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1620   -0.4505   -1.3646 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7701    0.6429    0.0803 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1928   -2.0476    0.1567 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7298   -1.0084    1.5815 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  3
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  2  0
  8  9  2  0
  1 10  1  0
  1 11  1  0
  2 12  1  0
  3 13  1  0
  3 14  1  0
  4 15  1  0
  4 16  1  0
  5 17  1  0
  5 18  1  0
  6 19  1  0
  6 20  1  0
M  END
Download

3D SDF for HMDB0038436 (6-Isothiocyanato-1-hexene)


  Mrv0541 05061310272D          

  9  8  0  0  0  0            999 V2000
    1.7605    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1895    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9039    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6184    1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3329    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.7618    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0474    1.8414    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    7.4763    1.0164    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  2  0  0  0  0
  3  2  1  0  0  0  0
  4  3  1  0  0  0  0
  5  4  1  0  0  0  0
  6  5  1  0  0  0  0
  8  6  1  0  0  0  0
  8  7  2  0  0  0  0
  9  7  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0038436

> <DATABASE_NAME>
hmdb

> <SMILES>
C=CCCCCN=C=S

> <INCHI_IDENTIFIER>
InChI=1S/C7H11NS/c1-2-3-4-5-6-8-7-9/h2H,1,3-6H2

> <INCHI_KEY>
WRFHVMFZOJHYGN-UHFFFAOYSA-N

> <FORMULA>
C7H11NS

> <MOLECULAR_WEIGHT>
141.234

> <EXACT_MASS>
141.061220047

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_AVERAGE_POLARIZABILITY>
16.59772262770347

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
6-isothiocyanatohex-1-ene

> <ALOGPS_LOGP>
3.46

> <JCHEM_LOGP>
2.9786984123333338

> <ALOGPS_LOGS>
-3.47

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
-2.7836589480761087

> <JCHEM_POLAR_SURFACE_AREA>
12.36

> <JCHEM_REFRACTIVITY>
44.4488

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.82e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
6-isothiocyanatohex-1-ene

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0038436 (6-Isothiocyanato-1-hexene)

HMDB0038436
     RDKit          3D
6-Isothiocyanato-1-hexene
 20 19  0  0  0  0  0  0  0  0999 V2000
   -2.8216    1.4489   -0.1678 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6488    0.9956   -0.6017 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4760   -0.4160   -1.0118 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4461   -1.1096   -0.1579 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8546   -0.4176   -0.2992 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9742   -1.0264    0.5034 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1632   -0.2331    0.2508 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.1344    0.9773    0.6757 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4685    2.5134    1.0327 S   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9034    2.4808    0.1199 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6431    0.7536   -0.1247 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7909    1.6545   -0.6690 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1570   -0.3855   -2.0906 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4407   -0.9656   -1.0262 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7915   -1.2561    0.8728 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3304   -2.1506   -0.5772 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1620   -0.4505   -1.3646 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7701    0.6429    0.0803 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1928   -2.0476    0.1567 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7298   -1.0084    1.5815 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  3
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  2  0
  8  9  2  0
  1 10  1  0
  1 11  1  0
  2 12  1  0
  3 13  1  0
  3 14  1  0
  4 15  1  0
  4 16  1  0
  5 17  1  0
  5 18  1  0
  6 19  1  0
  6 20  1  0
M  END
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PDB for HMDB0038436 (6-Isothiocyanato-1-hexene)

HEADER    PROTEIN                                 06-MAY-13   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-MAY-13         0                                  
HETATM    1  C   UNK     0       3.286   3.437   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       4.620   2.667   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       5.954   3.437   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       7.287   2.667   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       8.621   3.437   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       9.955   2.667   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      12.622   2.667   0.000  0.00  0.00           C+0
HETATM    8  N   UNK     0      11.288   3.437   0.000  0.00  0.00           N+0
HETATM    9  S   UNK     0      13.956   1.897   0.000  0.00  0.00           S+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    8                                                       
CONECT    7    8    9                                                       
CONECT    8    6    7                                                       
CONECT    9    7                                                            
MASTER        0    0    0    0    0    0    0    0    9    0   16    0
END
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3D PDB for HMDB0038436 (6-Isothiocyanato-1-hexene)

COMPND    HMDB0038436
HETATM    1  C1  UNL     1      -2.822   1.449  -0.168  1.00  0.00           C  
HETATM    2  C2  UNL     1      -1.649   0.996  -0.602  1.00  0.00           C  
HETATM    3  C3  UNL     1      -1.476  -0.416  -1.012  1.00  0.00           C  
HETATM    4  C4  UNL     1      -0.446  -1.110  -0.158  1.00  0.00           C  
HETATM    5  C5  UNL     1       0.855  -0.418  -0.299  1.00  0.00           C  
HETATM    6  C6  UNL     1       1.974  -1.026   0.503  1.00  0.00           C  
HETATM    7  N1  UNL     1       3.163  -0.233   0.251  1.00  0.00           N  
HETATM    8  C7  UNL     1       3.134   0.977   0.676  1.00  0.00           C  
HETATM    9  S1  UNL     1       3.469   2.513   1.033  1.00  0.00           S  
HETATM   10  H1  UNL     1      -2.903   2.481   0.120  1.00  0.00           H  
HETATM   11  H2  UNL     1      -3.643   0.754  -0.125  1.00  0.00           H  
HETATM   12  H3  UNL     1      -0.791   1.655  -0.669  1.00  0.00           H  
HETATM   13  H4  UNL     1      -1.157  -0.385  -2.091  1.00  0.00           H  
HETATM   14  H5  UNL     1      -2.441  -0.966  -1.026  1.00  0.00           H  
HETATM   15  H6  UNL     1      -0.792  -1.256   0.873  1.00  0.00           H  
HETATM   16  H7  UNL     1      -0.330  -2.151  -0.577  1.00  0.00           H  
HETATM   17  H8  UNL     1       1.162  -0.451  -1.365  1.00  0.00           H  
HETATM   18  H9  UNL     1       0.770   0.643   0.080  1.00  0.00           H  
HETATM   19  H10 UNL     1       2.193  -2.048   0.157  1.00  0.00           H  
HETATM   20  H11 UNL     1       1.730  -1.008   1.581  1.00  0.00           H  
CONECT    1    2    2   10   11
CONECT    2    3   12
CONECT    3    4   13   14
CONECT    4    5   15   16
CONECT    5    6   17   18
CONECT    6    7   19   20
CONECT    7    8    8
CONECT    8    9    9
END
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SMILES for HMDB0038436 (6-Isothiocyanato-1-hexene)

C=CCCCCN=C=S
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INCHI for HMDB0038436 (6-Isothiocyanato-1-hexene)

InChI=1S/C7H11NS/c1-2-3-4-5-6-8-7-9/h2H,1,3-6H2
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View in JSmolView Stereo Labels
Synonyms
ValueSource
5-Hexenyl isothiocyanateHMDB, MeSH
5-HeITCMeSH
Chemical FormulaC7H11NS
Average Molecular Weight141.234
Monoisotopic Molecular Weight141.061220047
IUPAC Name6-isothiocyanatohex-1-ene
Traditional Name6-isothiocyanatohex-1-ene
CAS Registry Number49776-81-0
SMILES
C=CCCCCN=C=S
InChI Identifier
InChI=1S/C7H11NS/c1-2-3-4-5-6-8-7-9/h2H,1,3-6H2
InChI KeyWRFHVMFZOJHYGN-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as isothiocyanates. These are organic compounds containing the isothiocyanate group, an isocyanate analogue with the general formula RN=C=S.
KingdomOrganic compounds
Super ClassOrganosulfur compounds
ClassIsothiocyanates
Sub ClassNot Available
Direct ParentIsothiocyanates
Alternative Parents
Substituents
  • Isothiocyanate
  • Organic 1,3-dipolar compound
  • Propargyl-type 1,3-dipolar organic compound
  • Organic nitrogen compound
  • Organopnictogen compound
  • Hydrocarbon derivative
  • Organonitrogen compound
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
Biological locationRoute of exposureSource
ProcessNot Available
Role
Biological role
Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling Point213.00 to 214.00 °C. @ 760.00 mm HgThe Good Scents Company Information System
Water Solubility0 slightlyThe Good Scents Company Information System
LogP3.416 (est)The Good Scents Company Information System
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility0.048 g/LALOGPS
logP3.46ALOGPS
logP2.98ChemAxon
logS-3.5ALOGPS
pKa (Strongest Basic)-2.8ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count1ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area12.36 ŲChemAxon
Rotatable Bond Count5ChemAxon
Refractivity44.45 m³·mol⁻¹ChemAxon
Polarizability16.6 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DarkChem[M+H]+131.66931661259
DarkChem[M-H]-128.39131661259
DeepCCS[M+H]+135.45830932474
DeepCCS[M-H]-133.34230932474
DeepCCS[M-2H]-168.92230932474
DeepCCS[M+Na]+143.39630932474
AllCCS[M+H]+132.432859911
AllCCS[M+H-H2O]+128.332859911
AllCCS[M+NH4]+136.232859911
AllCCS[M+Na]+137.332859911
AllCCS[M-H]-135.832859911
AllCCS[M+Na-2H]-138.532859911
AllCCS[M+HCOO]-141.632859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
6-Isothiocyanato-1-hexeneC=CCCCCN=C=S1676.1Standard polar33892256
6-Isothiocyanato-1-hexeneC=CCCCCN=C=S1159.6Standard non polar33892256
6-Isothiocyanato-1-hexeneC=CCCCCN=C=S1169.9Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - 6-Isothiocyanato-1-hexene GC-MS (Non-derivatized) - 70eV, Positivesplash10-059f-9000000000-f14d415d4d9fc3da846f2017-09-01Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 6-Isothiocyanato-1-hexene GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 6-Isothiocyanato-1-hexene 10V, Positive-QTOFsplash10-0006-4900000000-866603d42b4460ac888d2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 6-Isothiocyanato-1-hexene 20V, Positive-QTOFsplash10-001l-9300000000-2ac181968f964d54c3892016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 6-Isothiocyanato-1-hexene 40V, Positive-QTOFsplash10-0006-9000000000-7715db68ecbc6d88e0c22016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 6-Isothiocyanato-1-hexene 10V, Negative-QTOFsplash10-0006-2900000000-f70ceef1daca05e4bc1f2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 6-Isothiocyanato-1-hexene 20V, Negative-QTOFsplash10-052f-9600000000-9bf881c69fcd642f1f882016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 6-Isothiocyanato-1-hexene 40V, Negative-QTOFsplash10-0a4i-9000000000-d11d4d4ad65f15f52ba82016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 6-Isothiocyanato-1-hexene 10V, Positive-QTOFsplash10-0a4l-9400000000-c2e9750d06a148c955962021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 6-Isothiocyanato-1-hexene 20V, Positive-QTOFsplash10-0a4i-9000000000-9a510efd6751d63a017a2021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 6-Isothiocyanato-1-hexene 40V, Positive-QTOFsplash10-05fr-9000000000-5aeb691119efb24daf1d2021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 6-Isothiocyanato-1-hexene 10V, Negative-QTOFsplash10-0a4i-9000000000-286b63d3516de7d14a122021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 6-Isothiocyanato-1-hexene 20V, Negative-QTOFsplash10-0a4i-9000000000-286b63d3516de7d14a122021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 6-Isothiocyanato-1-hexene 40V, Negative-QTOFsplash10-0a4i-9000000000-286b63d3516de7d14a122021-09-22Wishart LabView Spectrum

IR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted IR SpectrumIR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+H]+)2023-02-04FELIX labView Spectrum
Predicted IR SpectrumIR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+Na]+)2023-02-04FELIX labView Spectrum
Biological Properties
Cellular Locations
  • Membrane
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB017794
KNApSAcK IDNot Available
Chemspider ID160714
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound184852
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1586791
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. (). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .