Np mrd loader

Showing NP-Card for L-Homocysteine (NP0334659)

Jump To Section:
IdentificationSpectraBioTaxonomyChemoTaxonomyPhysical propertiesLinksReferencesXML
Record Information
Version2.0
Created at2024-09-10 19:21:10 UTC
Updated at2024-09-10 19:21:10 UTC
NP-MRD IDNP0334659
Secondary Accession NumbersNone
Natural Product Identification
Common NameL-Homocysteine
DescriptionL-Homocysteine belongs to the class of organic compounds known as alpha amino acids. These are amino acids in which the amino group is attached to the carbon atom immediately adjacent to the carboxylate group (alpha carbon). L-Homocysteine was first documented in 2024 (PMID: 39312861). Based on a literature review a small amount of articles have been published on L-Homocysteine (PMID: 39311576) (PMID: 39293623) (PMID: 39292980) (PMID: 39282651).
Structure
Thumb
MOLSDFPDBSMILESInChI

MOL for NP0334659 (L-Homocysteine)


  Mrv2104 05252321532D          

  8  7  0  0  0  0            999 V2000
   23.7337  -12.6807    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
   25.8772  -10.6181    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   25.1627   -9.3806    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   23.7337  -10.2056    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   24.4482  -10.6181    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   24.4482  -11.4431    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   23.7337  -11.8556    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   25.1627  -10.2056    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  7  1  0  0  0  0
  2  8  1  0  0  0  0
  3  8  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  5  8  1  0  0  0  0
  6  7  1  0  0  0  0
M  END
Download

3D MOL for NP0334659 (L-Homocysteine)

Download
3D SDF for NP0334659 (L-Homocysteine)

  Mrv2104 05252321532D          

  8  7  0  0  0  0            999 V2000
   23.7337  -12.6807    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
   25.8772  -10.6181    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   25.1627   -9.3806    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   23.7337  -10.2056    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   24.4482  -10.6181    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   24.4482  -11.4431    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   23.7337  -11.8556    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   25.1627  -10.2056    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  7  1  0  0  0  0
  2  8  1  0  0  0  0
  3  8  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  5  8  1  0  0  0  0
  6  7  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0334659

> <DATABASE_NAME>
NP-MRD

> <SMILES>
NC(CCS)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1/C4H9NO2S/c5-3(1-2-8)4(6)7/h3,8H,1-2,5H2,(H,6,7)

> <INCHI_KEY>
FFFHZYDWPBMWHY-UHFFFAOYNA-N

> <FORMULA>
C4H9NO2S

> <MOLECULAR_WEIGHT>
135.18

> <EXACT_MASS>
135.035399708

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
17

> <JCHEM_AVERAGE_POLARIZABILITY>
13.536000164201784

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-amino-4-sulfanylbutanoic acid

> <JCHEM_LOGP>
-2.5764673824810185

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
10.279400411474743

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.458553724459435

> <JCHEM_PKA_STRONGEST_BASIC>
9.413365429707895

> <JCHEM_POLAR_SURFACE_AREA>
63.32000000000001

> <JCHEM_REFRACTIVITY>
32.935

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
homocysteine

> <JCHEM_VEBER_RULE>
0

$$$$

Download
3D-SDF for NP0334659 (L-Homocysteine)
Download
PDB for NP0334659 (L-Homocysteine)
HEADER    PROTEIN                                 25-MAY-23   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   25-MAY-23         0                                  
HETATM    1  S   UNK     0      44.303 -23.671   0.000  0.00  0.00           S+0
HETATM    2  O   UNK     0      48.304 -19.820   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0      46.970 -17.510   0.000  0.00  0.00           O+0
HETATM    4  N   UNK     0      44.303 -19.050   0.000  0.00  0.00           N+0
HETATM    5  C   UNK     0      45.637 -19.820   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      45.637 -21.360   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      44.303 -22.130   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      46.970 -19.050   0.000  0.00  0.00           C+0
CONECT    1    7                                                            
CONECT    2    8                                                            
CONECT    3    8                                                            
CONECT    4    5                                                            
CONECT    5    4    6    8                                                  
CONECT    6    5    7                                                       
CONECT    7    1    6                                                       
CONECT    8    2    3    5                                                  
MASTER        0    0    0    0    0    0    0    0    8    0   14    0
END

Download
3D PDB for NP0334659 (L-Homocysteine)
Download
SMILES for NP0334659 (L-Homocysteine)
NC(CCS)C(O)=O
Download
INCHI for NP0334659 (L-Homocysteine)
InChI=1/C4H9NO2S/c5-3(1-2-8)4(6)7/h3,8H,1-2,5H2,(H,6,7)
Download
View in JSmol
SynonymsNot Available
Chemical FormulaC4H9NO2S
Average Mass135.1800 Da
Monoisotopic Mass135.03540 Da
IUPAC Name2-amino-4-sulfanylbutanoic acid
Traditional Namehomocysteine
CAS Registry NumberNot Available
SMILES
NC(CCS)C(O)=O
InChI Identifier
InChI=1/C4H9NO2S/c5-3(1-2-8)4(6)7/h3,8H,1-2,5H2,(H,6,7)
InChI KeyFFFHZYDWPBMWHY-UHFFFAOYNA-N
Experimental Spectra
Not Available
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of OriginNot Available
Chemical Taxonomy
DescriptionThis compound belongs to the class of organic compounds known as alpha amino acids. These are amino acids in which the amino group is attached to the carbon atom immediately adjacent to the carboxylate group (alpha carbon).
KingdomOrganic compounds  
Super ClassOrganic acids and derivatives  
ClassCarboxylic acids and derivatives  
Sub ClassAmino acids, peptides, and analogues  
Direct ParentAlpha amino acids  
Alternative Parents
Substituents
  • Alpha-amino acid
    • 

  • Thia fatty acid
    • 

  • Fatty acyl
    • 

  • Fatty acid
    • 

  • Amino acid
    • 

  • Alkylthiol
    • 

  • Carboxylic acid
    • 

  • Monocarboxylic acid or derivatives
    • 

  • Organic nitrogen compound
    • 

  • Hydrocarbon derivative
    • 

  • Primary amine
    • 

  • Organosulfur compound
    • 

  • Organooxygen compound
    • 

  • Organonitrogen compound
    • 

  • Organic oxide
    • 

  • Primary aliphatic amine
    • 

  • Organopnictogen compound
    • 

  • Carbonyl group
    • 

  • Amine
    • 

  • Organic oxygen compound
    • 

  • 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-2.6ChemAxon
pKa (Strongest Acidic)2.46ChemAxon
pKa (Strongest Basic)9.41ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area63.32 ŲChemAxon
Rotatable Bond Count3ChemAxon
Refractivity32.94 m³·mol⁻¹ChemAxon
Polarizability13.54 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 IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkHomocysteine  
METLIN IDNot Available
PubChem CompoundNot Available
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. Sun WD, Zhu XJ, Li JJ, Mei YZ, Li WS, Li JH: Nicotinamide N-methyltransferase (NNMT): A key enzyme in cancer metabolism and therapeutic target. Int Immunopharmacol. 2024 Sep 22;142(Pt B):113208. doi:  10.1016/j.intimp.2024.113208. [PubMed:39312861  ] 
  2. Hasebe F, Adachi K, Maruyama C, Hamano Y: Discovery of a novel methionine biosynthetic route via O-phospho-l-homoserine. Appl Environ Microbiol. 2024 Sep 23:e0124724. doi: 10.1128/aem.01247-24. [PubMed:39311576  ] 
  3. Qin Z, Liu H, Zhao P, Wang K, Ren H, Miao C, Li J, Chen YZ, Chen Z: SLAM: Structure-aware lysine beta-hydroxybutyrylation prediction with protein language model. Int J Biol Macromol. 2024 Sep 16;280(Pt 1):135741. doi:  10.1016/j.ijbiomac.2024.135741. [PubMed:39293623  ] 
  4. Schwiertz D, Angelina J, Zhang H, Barz M: Miktoarm Star-polypept(o)ide-Based Polyion Complex Micelles for the Delivery of Large Nucleic Acids. Biomacromolecules. 2024 Sep 18. doi: 10.1021/acs.biomac.4c00695. [PubMed:39292980  ] 
  5. Wen X, Leopold V, Seebeck FP: Enzymatic synthesis of S-adenosyl-l-homocysteine and its nucleoside analogs from racemic homocysteine thiolactone. Chem Sci. 2024 Sep 6. doi: 10.1039/d4sc03801k. [PubMed:39282651  ]