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Showing NP-Card for d-leucine (NP0194232)

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Record Information
Version2.0
Created at2022-09-04 11:51:40 UTC
Updated at2025-07-18 00:04:12 UTC
NP-MRD IDNP0194232
Natural Product DOIhttps://doi.org/10.57994/4341
Secondary Accession NumbersNone
Natural Product Identification
Common Named-leucine
DescriptionD-Leucine, also known as (R)-leucine or D-leucin, belongs to the class of organic compounds known as leucine and derivatives. Leucine and derivatives are compounds containing leucine or a derivative thereof resulting from reaction of leucine at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom. D-Leucine is a very strong basic compound (based on its pKa). D-Leucine exists in all eukaryotes, ranging from yeast to humans. d-leucine was first documented in 2011 (PMID: 21941889). The D-enantiomer of leucine (PMID: 24097941).
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0194232 (d-leucine)


  Mrv1652304062013012D          

  9  8  0  0  1  0            999 V2000
   -0.1914    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5230    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5230    1.9520    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9520    1.1270    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.9520    1.9520    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3809    1.1270    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664   -0.1105    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  2  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  1  0  0  0
  5  7  1  0  0  0  0
  7  8  1  0  0  0  0
  7  9  2  0  0  0  0
M  END
Download

3D MOL for NP0194232 (d-leucine)

     RDKit          3D

 22 21  0  0  0  0  0  0  0  0999 V2000
   -2.1466    1.0246    0.9538 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1411   -0.0892    0.6438 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6840   -0.8593   -0.5280 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1397    0.5876    0.2469 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2331   -0.3929   -0.0904 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.8349   -1.2309   -1.1857 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.4397    0.3962   -0.4470 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9450    0.2533   -1.5899 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0443    1.2877    0.4159 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7133    1.6842    1.7534 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0945    0.5671    1.2501 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2548    1.6184    0.0189 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9776   -0.7342    1.5086 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8103   -0.7823   -0.5126 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3831   -0.4280   -1.5020 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4234   -1.9397   -0.4326 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0166    1.2155   -0.6643 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5292    1.2452    1.0513 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4757   -1.0090    0.8004 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9122   -2.2430   -0.8942 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4980   -1.0944   -1.9832 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5933    0.9230    1.1870 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  5  6  1  0
  5  7  1  0
  7  9  1  0
  7  8  2  0
  1 10  1  0
  1 11  1  0
  1 12  1  0
  2 13  1  0
  3 14  1  0
  3 15  1  0
  3 16  1  0
  4 17  1  0
  4 18  1  0
  5 19  1  1
  6 20  1  0
  6 21  1  0
  9 22  1  0
M  END
Download

3D SDF for NP0194232 (d-leucine)


  Mrv1652304062013012D          

  9  8  0  0  1  0            999 V2000
   -0.1914    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5230    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5230    1.9520    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9520    1.1270    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.9520    1.9520    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3809    1.1270    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664   -0.1105    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  2  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  1  0  0  0
  5  7  1  0  0  0  0
  7  8  1  0  0  0  0
  7  9  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0194232

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C6H13NO2/c1-4(2)3-5(7)6(8)9/h4-5H,3,7H2,1-2H3,(H,8,9)/t5-/m1/s1

> <INCHI_KEY>
ROHFNLRQFUQHCH-RXMQYKEDSA-N

> <FORMULA>
C6H13NO2

> <MOLECULAR_WEIGHT>
131.1729

> <EXACT_MASS>
131.094628665

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
22

> <JCHEM_AVERAGE_POLARIZABILITY>
14.245654175557164

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R)-2-amino-4-methylpentanoic acid

> <ALOGPS_LOGP>
-1.82

> <JCHEM_LOGP>
-1.5861571715466434

> <ALOGPS_LOGS>
-0.27

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.787708882185853

> <JCHEM_PKA_STRONGEST_BASIC>
9.51901425787269

> <JCHEM_POLAR_SURFACE_AREA>
63.32

> <JCHEM_REFRACTIVITY>
34.1709

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.98e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
L-(+)-leucine

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0194232 (d-leucine)

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PDB for NP0194232 (d-leucine)
HEADER    PROTEIN                                 06-APR-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-APR-20         0                                  
HETATM    1  C   UNK     0      -0.357   1.334   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.976   2.104   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.976   3.644   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.310   1.334   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       3.644   2.104   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0       3.644   3.644   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0       4.977   1.334   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       6.311   2.104   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0       4.977  -0.206   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5                                                       
CONECT    5    4    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5    8    9                                                  
CONECT    8    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 NP0194232 (d-leucine)
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SMILES for NP0194232 (d-leucine)
CC(C)C[C@@H](N)C(O)=O
Download
INCHI for NP0194232 (d-leucine)
InChI=1S/C6H13NO2/c1-4(2)3-5(7)6(8)9/h4-5H,3,7H2,1-2H3,(H,8,9)/t5-/m1/s1
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View in JSmol
Synonyms
ValueSource
(2R)-2-Amino-4-methylpentanoic acidChEBI
(R)-(-)-LeucineChEBI
(R)-LeucineChEBI
D-2-Amino-4-methylvaleric acidChEBI
D-LeucinChEBI
D-LeuzinChEBI
DLEChEBI
(2R)-2-Amino-4-methylpentanoateGenerator
D-2-Amino-4-methylvalerateGenerator
(R)-(−)-leucineHMDB
Chemical FormulaC6H13NO2
Average Mass131.1729 Da
Monoisotopic Mass131.09463 Da
IUPAC Name(2R)-2-amino-4-methylpentanoic acid
Traditional NameL-(+)-leucine
CAS Registry NumberNot Available
SMILES
CC(C)C[C@@H](N)C(O)=O
InChI Identifier
InChI=1S/C6H13NO2/c1-4(2)3-5(7)6(8)9/h4-5H,3,7H2,1-2H3,(H,8,9)/t5-/m1/s1
InChI KeyROHFNLRQFUQHCH-RXMQYKEDSA-N
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
COSY NMR[1H, 1H] NMR Spectrum (2D, 600 MHz, C2D6OS, experimental)Not AvailableSumner lab, University of MissouriRonald Myers2025-07-16View Spectrum
HSQC NMR[1H, 13C] NMR Spectrum (2D, 600 MHz, C2D6OS, experimental)Not AvailableSumner lab, University of MissouriRonald Myers2025-07-16View Spectrum
HMBC NMR[1H, 13C] NMR Spectrum (2D, 600 MHz, C2D6OS, experimental)Not AvailableSumner lab, University of MissouriRonald Myers2025-07-16View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, C2D6OS, experimental)Not AvailableSumner lab, University of MissouriRonald Myers2025-07-16View Spectrum
1D NMR1H NMR Spectrum (1D, 600.0 MHz, C2D6OS, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Predicted Spectra
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 25 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 100 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 252 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 1000 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 50 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 200 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 75 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 300 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 101 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 126 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 151 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 176 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 700 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 201 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 800 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 226 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 900 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Chemical Shift Submissions
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR1H NMR Spectrum (1D, 600.0, C2D6OS, simulated)rjm4kd@umsystem.eduSumner lab, University of MissouriRonald Myers2025-07-16View Spectrum
Species
Species of OriginNot Available
Chemical Taxonomy
Description Belongs to the class of organic compounds known as leucine and derivatives. Leucine and derivatives are compounds containing leucine or a derivative thereof resulting from reaction of leucine at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom.
KingdomOrganic compounds  
Super ClassOrganic acids and derivatives  
ClassCarboxylic acids and derivatives  
Sub ClassAmino acids, peptides, and analogues  
Direct ParentLeucine and derivatives  
Alternative Parents
Substituents
  • Leucine or derivatives
    • 

  • Alpha-amino acid
    • 

  • D-alpha-amino acid
    • 

  • Branched fatty acid
    • 

  • Methyl-branched fatty acid
    • 

  • Fatty acid
    • 

  • Fatty acyl
    • 

  • Amino acid
    • 

  • Monocarboxylic acid or derivatives
    • 

  • Carboxylic acid
    • 

  • Organic oxide
    • 

  • Organopnictogen compound
    • 

  • Primary amine
    • 

  • Organooxygen compound
    • 

  • Organonitrogen compound
    • 

  • Primary aliphatic amine
    • 

  • Carbonyl group
    • 

  • Organic oxygen compound
    • 

  • Amine
    • 

  • Organic nitrogen compound
    • 

  • Hydrocarbon derivative
    • 

  • 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
logP-1.8ALOGPS
logP-1.6ChemAxon
logS-0.27ALOGPS
pKa (Strongest Acidic)2.79ChemAxon
pKa (Strongest Basic)9.52ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area63.32 ŲChemAxon
Rotatable Bond Count3ChemAxon
Refractivity34.17 m³·mol⁻¹ChemAxon
Polarizability14.25 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0013773  
DrugBank IDDB01746  
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID388617  
KEGG Compound IDC01570  
BioCyc IDCPD-12150  
BiGG IDNot Available
Wikipedia LinkLeucine  
METLIN IDNot Available
PubChem Compound439524  
PDB IDDLE  
ChEBI ID28225  
Good Scents IDNot Available
References
General References
  1. Ohlendorf B, Simon S, Wiese J, Imhoff JF: Szentiamide, an N-formylated cyclic depsipeptide from Xenorhabdus szentirmaii DSM 16338T. Nat Prod Commun. 2011 Sep;6(9):1247-50. [PubMed:21941889  ] 
  2. Leiman SA, May JM, Lebar MD, Kahne D, Kolter R, Losick R: D-amino acids indirectly inhibit biofilm formation in Bacillus subtilis by interfering with protein synthesis. J Bacteriol. 2013 Dec;195(23):5391-5. doi: 10.1128/JB.00975-13. Epub 2013 Oct 4. [PubMed:24097941  ] 
  3. LOTUS database [Link]