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Showing NP-Card for (R)-2-Hydroxybutyric acid (NP0002710)

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Record Information
Version1.0
Created at2020-11-23 19:38:30 UTC
Updated at2021-08-12 19:51:55 UTC
NP-MRD IDNP0002710
Secondary Accession NumbersNone
Natural Product Identification
Common Name(R)-2-Hydroxybutyric acid
Provided ByBMRBBMRB logo
Description(R)-2-hydroxybutyric acid is also known as (R)-2-hydroxybutanoate. It was first documented in 2008 (PMID: 17984079). Based on a literature review very few articles have been published on (R)-2-hydroxybutyric acid (PMID: 33376359) (PMID: 24297001) (PMID: 20014430).
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for NP0002710 ((R)-2-Hydroxybutyric acid)


     RDKit          2D

 15 14  0  0  0  0  0  0  0  0999 V2000
   -2.0078    0.6418    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6950   -0.0837    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6179   -0.8093    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1076   -2.1221    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3434    0.5036    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7316    1.8731    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8432    0.5317    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2823    1.9546    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7333   -0.6711    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3207    1.3673    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4205   -1.3966    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1349    1.3078    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9308   -1.5348    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6666   -3.4069    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5687    1.8446    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
  3  5  1  0
  5  6  2  0
  5  7  1  0
  1  8  1  1
  1  9  1  0
  1 10  1  0
  2 11  1  1
  2 12  1  0
  3 13  1  1
  4 14  1  0
  7 15  1  0
M  END
Download

3D MOL for NP0002710 ((R)-2-Hydroxybutyric acid)

NP0002710
     RDKit          3D

 15 14  0  0  0  0  0  0  0  0999 V2000
    1.6180   -0.5292    0.0293 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5915    0.1016    0.9243 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5601    0.6598    0.0777 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.0175    1.6027   -0.7698 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1496   -0.4254   -0.7271 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0842   -0.4042   -1.9806 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7939   -1.5033   -0.1361 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4962   -0.7879    0.6400 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2119   -1.4048   -0.5218 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9247    0.2386   -0.7245 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0859    0.9531    1.4488 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2225   -0.5803    1.7023 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3181    1.1295    0.7060 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4843    2.4404   -0.7707 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7780   -1.4906    0.1021 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
  3  5  1  0
  5  6  2  0
  5  7  1  0
  1  8  1  0
  1  9  1  0
  1 10  1  0
  2 11  1  0
  2 12  1  0
  3 13  1  1
  4 14  1  0
  7 15  1  0
M  END
Download

3D SDF for NP0002710 ((R)-2-Hydroxybutyric acid)


     RDKit          2D

 15 14  0  0  0  0  0  0  0  0999 V2000
   -2.0078    0.6418    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6950   -0.0837    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6179   -0.8093    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1076   -2.1221    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3434    0.5036    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7316    1.8731    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8432    0.5317    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2823    1.9546    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7333   -0.6711    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3207    1.3673    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4205   -1.3966    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1349    1.3078    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9308   -1.5348    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6666   -3.4069    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5687    1.8446    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
  3  5  1  0
  5  6  2  0
  5  7  1  0
  1  8  1  1
  1  9  1  0
  1 10  1  0
  2 11  1  1
  2 12  1  0
  3 13  1  1
  4 14  1  0
  7 15  1  0
M  END
> <DATABASE_ID>
NP0002710

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C4H8O3/c1-2-3(5)4(6)7/h3,5H,2H2,1H3,(H,6,7)/t3-/m1/s1

> <INCHI_KEY>
AFENDNXGAFYKQO-GSVOUGTGSA-N

> <FORMULA>
C4H8O3

> <MOLECULAR_WEIGHT>
104.105

> <EXACT_MASS>
104.047344118

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
15

> <JCHEM_AVERAGE_POLARIZABILITY>
9.972009147437083

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R)-2-hydroxybutanoic acid

> <JCHEM_LOGP>
0.050692876999999914

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
14.293154365104638

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.989998858113875

> <JCHEM_PKA_STRONGEST_BASIC>
-3.7935876935907205

> <JCHEM_POLAR_SURFACE_AREA>
57.53

> <JCHEM_REFRACTIVITY>
23.3638

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(R)-2-hydroxybutyric acid

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for NP0002710 ((R)-2-Hydroxybutyric acid)

NP0002710
     RDKit          3D

 15 14  0  0  0  0  0  0  0  0999 V2000
    1.6180   -0.5292    0.0293 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5915    0.1016    0.9243 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5601    0.6598    0.0777 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.0175    1.6027   -0.7698 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1496   -0.4254   -0.7271 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0842   -0.4042   -1.9806 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7939   -1.5033   -0.1361 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4962   -0.7879    0.6400 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2119   -1.4048   -0.5218 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9247    0.2386   -0.7245 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0859    0.9531    1.4488 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2225   -0.5803    1.7023 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3181    1.1295    0.7060 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4843    2.4404   -0.7707 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7780   -1.4906    0.1021 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
  3  5  1  0
  5  6  2  0
  5  7  1  0
  1  8  1  0
  1  9  1  0
  1 10  1  0
  2 11  1  0
  2 12  1  0
  3 13  1  1
  4 14  1  0
  7 15  1  0
M  END
Download

PDB for NP0002710 ((R)-2-Hydroxybutyric 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       2.310   4.001   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.540   2.667   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.310   1.334   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.540   0.000   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       3.850   1.334   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0       2.310  -1.334   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4    5                                                  
CONECT    4    3    6    7                                                  
CONECT    5    3                                                            
CONECT    6    4                                                            
CONECT    7    4                                                            
MASTER        0    0    0    0    0    0    0    0    7    0   12    0
END
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3D PDB for NP0002710 ((R)-2-Hydroxybutyric acid)

COMPND    NP0002710
HETATM    1  C1  UNL     1       1.618  -0.529   0.029  1.00  0.00           C  
HETATM    2  C2  UNL     1       0.591   0.102   0.924  1.00  0.00           C  
HETATM    3  C3  UNL     1      -0.560   0.660   0.078  1.00  0.00           C  
HETATM    4  O1  UNL     1       0.018   1.603  -0.770  1.00  0.00           O  
HETATM    5  C4  UNL     1      -1.150  -0.425  -0.727  1.00  0.00           C  
HETATM    6  O2  UNL     1      -1.084  -0.404  -1.981  1.00  0.00           O  
HETATM    7  O3  UNL     1      -1.794  -1.503  -0.136  1.00  0.00           O  
HETATM    8  H1  UNL     1       2.496  -0.788   0.640  1.00  0.00           H  
HETATM    9  H2  UNL     1       1.212  -1.405  -0.522  1.00  0.00           H  
HETATM   10  H3  UNL     1       1.925   0.239  -0.725  1.00  0.00           H  
HETATM   11  H4  UNL     1       1.086   0.953   1.449  1.00  0.00           H  
HETATM   12  H5  UNL     1       0.223  -0.580   1.702  1.00  0.00           H  
HETATM   13  H6  UNL     1      -1.318   1.129   0.706  1.00  0.00           H  
HETATM   14  H7  UNL     1      -0.484   2.440  -0.771  1.00  0.00           H  
HETATM   15  H8  UNL     1      -2.778  -1.491   0.102  1.00  0.00           H  
CONECT    1    2    8    9   10
CONECT    2    3   11   12
CONECT    3    4    5   13
CONECT    4   14
CONECT    5    6    6    7
CONECT    7   15
END
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SMILES for NP0002710 ((R)-2-Hydroxybutyric acid)

CC[C@@H](O)C(O)=O
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INCHI for NP0002710 ((R)-2-Hydroxybutyric acid)

InChI=1S/C4H8O3/c1-2-3(5)4(6)7/h3,5H,2H2,1H3,(H,6,7)/t3-/m1/s1
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View in JSmol
Synonyms
ValueSource
(R)-2-Hydroxybutanoic acidChEBI
D-2-Hydroxybutanoic acidChEBI
D-2-Hydroxybutyric acidChEBI
(R)-2-HydroxybutanoateGenerator
D-2-HydroxybutanoateGenerator
D-2-HydroxybutyrateGenerator
(R)-2-HydroxybutyrateGenerator
Chemical FormulaC4H8O3
Average Mass104.1050 Da
Monoisotopic Mass104.04734 Da
IUPAC Name(2R)-2-hydroxybutanoic acid
Traditional Name(R)-2-hydroxybutyric acid
CAS Registry NumberNot Available
SMILES
CC[C@@H](O)C(O)=O
InChI Identifier
InChI=1S/C4H8O3/c1-2-3(5)4(6)7/h3,5H,2H2,1H3,(H,6,7)/t3-/m1/s1
InChI KeyAFENDNXGAFYKQO-GSVOUGTGSA-N
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 400 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
logP0.051ChemAxon
pKa (Strongest Acidic)3.99ChemAxon
pKa (Strongest Basic)-3.8ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area57.53 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity23.36 m³·mol⁻¹ChemAxon
Polarizability9.97 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 ID395841
KEGG Compound IDNot Available
BioCyc IDCPD-12253
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem CompoundNot Available
PDB IDNot Available
ChEBI ID50612
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 ]
  2. Li S, Liu J, Zhou J, Wang Y, Jin F, Chen X, Yang J, Chen Z: Urinary Metabolomic Profiling Reveals Biological Pathways and Predictive Signatures Associated with Childhood Asthma. J Asthma Allergy. 2020 Dec 18;13:713-724. doi: 10.2147/JAA.S281198. eCollection 2020. [PubMed:33376359 ]
  3. Liu F, Li C: Total synthesis of (S)-14-azacamptothecin. Org Biomol Chem. 2014 Jan 28;12(4):637-42. doi: 10.1039/c3ob41883a. [PubMed:24297001 ]
  4. Das S, Glenn JH 4th, Subramanian M: Enantioselective oxidation of 2-hydroxy carboxylic acids by glycolate oxidase and catalase coexpressed in methylotrophic Pichia pastoris. Biotechnol Prog. 2010 May-Jun;26(3):607-15. doi: 10.1002/btpr.363. [PubMed:20014430 ]