Np mrd loader

Showing NP-Card for 2-hydroxyhexanoic acid (NP0002798)

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Record Information
Version1.0
Created at2020-11-23 19:40:42 UTC
Updated at2021-08-12 19:52:10 UTC
NP-MRD IDNP0002798
Secondary Accession NumbersNone
Natural Product Identification
Common Name2-hydroxyhexanoic acid
Provided ByBMRBBMRB logo
Description It was first documented in 2008 (PMID: 17984079). Based on a literature review very few articles have been published on (2S)-2-hydroxyhexanoic acid.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for NP0002798 (2-hydroxyhexanoic acid)


     RDKit          2D

 21 20  0  0  0  0  0  0  0  0999 V2000
   -3.6944    0.2496    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2105    0.0306    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7265   -0.1884    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7574   -0.4074    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2413   -0.6264    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0223   -2.1103    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4603    0.8576    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4070    1.9255    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.8549    1.4099    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4754    1.7335    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9134   -1.2344    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1783    0.4685    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4295   -1.4534    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9915    1.5145    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5076    1.2955    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9455   -1.6723    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5384   -1.8913    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7939    1.0922    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7252   -0.8454    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1980   -3.0419    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0739    2.8938    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  5  7  1  0
  7  8  2  0
  7  9  1  0
  1 10  1  6
  1 11  1  0
  1 12  1  0
  2 13  1  6
  2 14  1  0
  3 15  1  6
  3 16  1  0
  4 17  1  6
  4 18  1  0
  5 19  1  6
  6 20  1  0
  9 21  1  0
M  END
Download

3D MOL for NP0002798 (2-hydroxyhexanoic acid)

NP0002798
     RDKit          3D

 21 20  0  0  0  0  0  0  0  0999 V2000
   -2.3777    1.0797   -0.6652 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1647   -0.1189    0.2274 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8807   -0.8258   -0.1474 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3190    0.0834   -0.0038 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5860   -0.6394   -0.3814 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.7138   -1.7308    0.4745 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7765    0.2257   -0.1984 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7020   -0.0412    0.6073 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8393    1.3863   -0.9763 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7019    1.0585   -1.5256 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4162    1.0909   -1.0538 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1958    2.0177   -0.0884 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2130    0.1458    1.2968 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9858   -0.8668    0.0516 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7740   -1.7041    0.5253 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0048   -1.1926   -1.1845 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4176    0.4106    1.0345 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1319    0.9776   -0.6268 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5890   -0.9973   -1.4163 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3373   -2.5612    0.0930 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3020    2.2021   -0.5976 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  5  7  1  0
  7  8  2  0
  7  9  1  0
  1 10  1  0
  1 11  1  0
  1 12  1  0
  2 13  1  0
  2 14  1  0
  3 15  1  0
  3 16  1  0
  4 17  1  0
  4 18  1  0
  5 19  1  6
  6 20  1  0
  9 21  1  0
M  END
Download

3D SDF for NP0002798 (2-hydroxyhexanoic acid)


     RDKit          2D

 21 20  0  0  0  0  0  0  0  0999 V2000
   -3.6944    0.2496    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2105    0.0306    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7265   -0.1884    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7574   -0.4074    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2413   -0.6264    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0223   -2.1103    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4603    0.8576    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4070    1.9255    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.8549    1.4099    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4754    1.7335    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9134   -1.2344    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1783    0.4685    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4295   -1.4534    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9915    1.5145    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5076    1.2955    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9455   -1.6723    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5384   -1.8913    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7939    1.0922    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7252   -0.8454    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1980   -3.0419    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0739    2.8938    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  5  7  1  0
  7  8  2  0
  7  9  1  0
  1 10  1  6
  1 11  1  0
  1 12  1  0
  2 13  1  6
  2 14  1  0
  3 15  1  6
  3 16  1  0
  4 17  1  6
  4 18  1  0
  5 19  1  6
  6 20  1  0
  9 21  1  0
M  END
> <DATABASE_ID>
NP0002798

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CCCC[C@H](O)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C6H12O3/c1-2-3-4-5(7)6(8)9/h5,7H,2-4H2,1H3,(H,8,9)/t5-/m0/s1

> <INCHI_KEY>
NYHNVHGFPZAZGA-YFKPBYRVSA-N

> <FORMULA>
C6H12O3

> <MOLECULAR_WEIGHT>
132.159

> <EXACT_MASS>
132.078644246

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
21

> <JCHEM_AVERAGE_POLARIZABILITY>
14.020725319908397

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S)-2-hydroxyhexanoic acid

> <JCHEM_LOGP>
0.939830207

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
14.284162726812554

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.257947363146006

> <JCHEM_PKA_STRONGEST_BASIC>
-3.797522654160839

> <JCHEM_POLAR_SURFACE_AREA>
57.53

> <JCHEM_REFRACTIVITY>
32.5658

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(2S)-2-hydroxyhexanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for NP0002798 (2-hydroxyhexanoic acid)

NP0002798
     RDKit          3D

 21 20  0  0  0  0  0  0  0  0999 V2000
   -2.3777    1.0797   -0.6652 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1647   -0.1189    0.2274 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8807   -0.8258   -0.1474 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3190    0.0834   -0.0038 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5860   -0.6394   -0.3814 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.7138   -1.7308    0.4745 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7765    0.2257   -0.1984 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7020   -0.0412    0.6073 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8393    1.3863   -0.9763 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7019    1.0585   -1.5256 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4162    1.0909   -1.0538 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1958    2.0177   -0.0884 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2130    0.1458    1.2968 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9858   -0.8668    0.0516 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7740   -1.7041    0.5253 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0048   -1.1926   -1.1845 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4176    0.4106    1.0345 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1319    0.9776   -0.6268 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5890   -0.9973   -1.4163 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3373   -2.5612    0.0930 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3020    2.2021   -0.5976 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  5  7  1  0
  7  8  2  0
  7  9  1  0
  1 10  1  0
  1 11  1  0
  1 12  1  0
  2 13  1  0
  2 14  1  0
  3 15  1  0
  3 16  1  0
  4 17  1  0
  4 18  1  0
  5 19  1  6
  6 20  1  0
  9 21  1  0
M  END
Download

PDB for NP0002798 (2-hydroxyhexanoic acid)

HEADER    PROTEIN                                 23-NOV-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-NOV-20         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  O   UNK     0       8.621   4.977   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0      11.288   3.437   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0       9.955   1.127   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    7                                                  
CONECT    6    5    8    9                                                  
CONECT    7    5                                                            
CONECT    8    6                                                            
CONECT    9    6                                                            
MASTER        0    0    0    0    0    0    0    0    9    0   16    0
END
Download

3D PDB for NP0002798 (2-hydroxyhexanoic acid)

COMPND    NP0002798
HETATM    1  C1  UNL     1      -2.378   1.080  -0.665  1.00  0.00           C  
HETATM    2  C2  UNL     1      -2.165  -0.119   0.227  1.00  0.00           C  
HETATM    3  C3  UNL     1      -0.881  -0.826  -0.147  1.00  0.00           C  
HETATM    4  C4  UNL     1       0.319   0.083  -0.004  1.00  0.00           C  
HETATM    5  C5  UNL     1       1.586  -0.639  -0.381  1.00  0.00           C  
HETATM    6  O1  UNL     1       1.714  -1.731   0.475  1.00  0.00           O  
HETATM    7  C6  UNL     1       2.777   0.226  -0.198  1.00  0.00           C  
HETATM    8  O2  UNL     1       3.702  -0.041   0.607  1.00  0.00           O  
HETATM    9  O3  UNL     1       2.839   1.386  -0.976  1.00  0.00           O  
HETATM   10  H1  UNL     1      -1.702   1.058  -1.526  1.00  0.00           H  
HETATM   11  H2  UNL     1      -3.416   1.091  -1.054  1.00  0.00           H  
HETATM   12  H3  UNL     1      -2.196   2.018  -0.088  1.00  0.00           H  
HETATM   13  H4  UNL     1      -2.213   0.146   1.297  1.00  0.00           H  
HETATM   14  H5  UNL     1      -2.986  -0.867   0.052  1.00  0.00           H  
HETATM   15  H6  UNL     1      -0.774  -1.704   0.525  1.00  0.00           H  
HETATM   16  H7  UNL     1      -1.005  -1.193  -1.184  1.00  0.00           H  
HETATM   17  H8  UNL     1       0.418   0.411   1.034  1.00  0.00           H  
HETATM   18  H9  UNL     1       0.132   0.978  -0.627  1.00  0.00           H  
HETATM   19  H10 UNL     1       1.589  -0.997  -1.416  1.00  0.00           H  
HETATM   20  H11 UNL     1       1.337  -2.561   0.093  1.00  0.00           H  
HETATM   21  H12 UNL     1       3.302   2.202  -0.598  1.00  0.00           H  
CONECT    1    2   10   11   12
CONECT    2    3   13   14
CONECT    3    4   15   16
CONECT    4    5   17   18
CONECT    5    6    7   19
CONECT    6   20
CONECT    7    8    8    9
CONECT    9   21
END
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SMILES for NP0002798 (2-hydroxyhexanoic acid)

CCCC[C@H](O)C(O)=O
Download

INCHI for NP0002798 (2-hydroxyhexanoic acid)

InChI=1S/C6H12O3/c1-2-3-4-5(7)6(8)9/h5,7H,2-4H2,1H3,(H,8,9)/t5-/m0/s1
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View in JSmol
Synonyms
ValueSource
(2S)-2-HydroxyhexanoateGenerator
Chemical FormulaC6H12O3
Average Mass132.1590 Da
Monoisotopic Mass132.07864 Da
IUPAC Name(2S)-2-hydroxyhexanoic acid
Traditional Name(2S)-2-hydroxyhexanoic acid
CAS Registry NumberNot Available
SMILES
CCCC[C@H](O)C(O)=O
InChI Identifier
InChI=1S/C6H12O3/c1-2-3-4-5(7)6(8)9/h5,7H,2-4H2,1H3,(H,8,9)/t5-/m0/s1
InChI KeyNYHNVHGFPZAZGA-YFKPBYRVSA-N
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of OriginNot Available
Chemical Taxonomy
ClassificationNot classified
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
logP0.94ChemAxon
pKa (Strongest Acidic)4.26ChemAxon
pKa (Strongest Basic)-3.8ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area57.53 ŲChemAxon
Rotatable Bond Count4ChemAxon
Refractivity32.57 m³·mol⁻¹ChemAxon
Polarizability14.02 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDNot Available
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID5367280
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem CompoundNot Available
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. Ulrich EL, Akutsu H, Doreleijers JF, Harano Y, Ioannidis YE, Lin J, Livny M, Mading S, Maziuk D, Miller Z, Nakatani E, Schulte CF, Tolmie DE, Kent Wenger R, Yao H, Markley JL: BioMagResBank. Nucleic Acids Res. 2008 Jan;36(Database issue):D402-8. doi: 10.1093/nar/gkm957. Epub 2007 Nov 4. [PubMed:17984079 ]