Np mrd loader

Showing NP-Card for Succinic aldehyde (NP0084416)

Jump To Section:
IdentificationSpectraBioTaxonomyChemoTaxonomyPhysical propertiesLinksReferencesXML
Record Information
Version2.0
Created at2022-04-29 05:08:53 UTC
Updated at2022-04-29 05:08:53 UTC
NP-MRD IDNP0084416
Secondary Accession NumbersNone
Natural Product Identification
Common NameSuccinic aldehyde
DescriptionSUCCINALDEHYDE, also known as succindialdehyde or butanedial, belongs to the class of organic compounds known as alpha-hydrogen aldehydes. These are aldehydes with the general formula HC(H)(R)C(=O)H, where R is an organyl group. Succinic aldehyde is found in Paraburkholderia phymatum. SUCCINALDEHYDE is an extremely weak basic (essentially neutral) compound (based on its pKa).
Structure
Thumb
MOL3D MOLSDFPDBSMILESInChI

MOL for NP0084416 (Succinic aldehyde)

 
  Mrv1652303121904062D          

  6  5  0  0  0  0            999 V2000
   15.1748  -19.9462    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.8893  -19.5337    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.6038  -19.9462    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.3183  -19.5337    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.0327  -19.9462    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.7473  -19.5337    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
M  END
Download

3D MOL for NP0084416 (Succinic aldehyde)

     RDKit          3D

 12 11  0  0  0  0  0  0  0  0999 V2000
    1.9478   -1.0371    0.9897 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8720   -0.0774    0.2581 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5727    0.3811   -0.2243 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5823   -0.4460    0.2777 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8282    0.1076   -0.2708 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7930    1.0666   -0.9900 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7737    0.4289   -0.0288 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3569    1.4557    0.0426 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5070    0.3547   -1.3488 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3879   -1.4853   -0.0699 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6759   -0.3983    1.3884 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7627   -0.3505   -0.0239 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
  2  7  1  0
  3  8  1  0
  3  9  1  0
  4 10  1  0
  4 11  1  0
  5 12  1  0
M  END
Download

3D SDF for NP0084416 (Succinic aldehyde)

 
  Mrv1652303121904062D          

  6  5  0  0  0  0            999 V2000
   15.1748  -19.9462    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.8893  -19.5337    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.6038  -19.9462    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.3183  -19.5337    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.0327  -19.9462    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.7473  -19.5337    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0084416

> <DATABASE_NAME>
NP-MRD

> <SMILES>
O=CCCC=O

> <INCHI_IDENTIFIER>
InChI=1S/C4H6O2/c5-3-1-2-4-6/h3-4H,1-2H2

> <INCHI_KEY>
PCSMJKASWLYICJ-UHFFFAOYSA-N

> <FORMULA>
C4H6O2

> <MOLECULAR_WEIGHT>
86.09

> <EXACT_MASS>
86.036779433

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
12

> <JCHEM_AVERAGE_POLARIZABILITY>
8.363165960887018

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
butanedial

> <ALOGPS_LOGP>
0.28

> <JCHEM_LOGP>
-0.7157154719999999

> <ALOGPS_LOGS>
0.28

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
14.551155440545674

> <JCHEM_PKA_STRONGEST_BASIC>
-6.652795922859695

> <JCHEM_POLAR_SURFACE_AREA>
34.14

> <JCHEM_REFRACTIVITY>
21.6862

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.64e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
butanedione

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for NP0084416 (Succinic aldehyde)

Download
PDB for NP0084416 (Succinic aldehyde)
HEADER    PROTEIN                                 12-MAR-19   NONE
TITLE     NULL                                                        
COMPND    MOLECULE:                                                   
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   12-MAR-19         0                                  
HETATM    1  O   UNK     0      28.326 -37.233   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0      29.660 -36.463   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      30.994 -37.233   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      32.327 -36.463   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      33.661 -37.233   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      34.995 -36.463   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5                                                            
MASTER        0    0    0    0    0    0    0    0    6    0   10    0
END

Download
3D PDB for NP0084416 (Succinic aldehyde)
Download
SMILES for NP0084416 (Succinic aldehyde)
O=CCCC=O
Download
INCHI for NP0084416 (Succinic aldehyde)
InChI=1S/C4H6O2/c5-3-1-2-4-6/h3-4H,1-2H2
Download
View in JSmol
Synonyms
ValueSource
SuccindialdehydeKegg
1,4-Butane dialdehydeMeSH
ButanedialMeSH
Chemical FormulaC4H6O2
Average Mass86.0900 Da
Monoisotopic Mass86.03678 Da
IUPAC Namebutanedial
Traditional Namebutanedione
CAS Registry NumberNot Available
SMILES
O=CCCC=O
InChI Identifier
InChI=1S/C4H6O2/c5-3-1-2-4-6/h3-4H,1-2H2
InChI KeyPCSMJKASWLYICJ-UHFFFAOYSA-N
Experimental Spectra
Not Available
Predicted Spectra
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 25 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 252 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 50 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 75 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 101 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 126 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 151 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 176 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 201 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 226 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Paraburkholderia phymatum-
Chemical Taxonomy
Description Belongs to the class of organic compounds known as alpha-hydrogen aldehydes. These are aldehydes with the general formula HC(H)(R)C(=O)H, where R is an organyl group.
KingdomOrganic compounds  
Super ClassOrganic oxygen compounds  
ClassOrganooxygen compounds  
Sub ClassCarbonyl compounds  
Direct ParentAlpha-hydrogen aldehydes  
Alternative Parents
Substituents
  • Alpha-hydrogen aldehyde
    • 

  • Organic oxide
    • 

  • Hydrocarbon derivative
    • 

  • Short-chain aldehyde
    • 

  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Physical Properties
StateNot Available
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP0.28ALOGPS
logP-0.72ChemAxon
logS0.28ALOGPS
pKa (Strongest Acidic)14.55ChemAxon
pKa (Strongest Basic)-6.7ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count2ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area34.14 ŲChemAxon
Rotatable Bond Count3ChemAxon
Refractivity21.69 m³·mol⁻¹ChemAxon
Polarizability8.36 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleNoChemAxon
HMDB IDNot Available
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDC16835  
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound12524  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General ReferencesNot Available