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Showing NP-Card for enduracididine (NP0178200)

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Record Information
Version2.0
Created at2022-09-03 16:09:07 UTC
Updated at2022-09-03 16:09:07 UTC
NP-MRD IDNP0178200
Secondary Accession NumbersNone
Natural Product Identification
Common Nameenduracididine
DescriptionL-enduracididine, also known as L-end compound, belongs to the class of organic compounds known as l-alpha-amino acids. These are alpha amino acids which have the L-configuration of the alpha-carbon atom. enduracididine is found in Streptomyces wadayamensis. enduracididine was first documented in 2005 (PMID: 16298295). Based on a literature review a small amount of articles have been published on L-enduracididine (PMID: 29473729) (PMID: 26551990).
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0178200 (enduracididine)


  Mrv1652309032218092D          

 12 12  0  0  1  0            999 V2000
    0.5678    1.9393    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.1143    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2352    0.6294    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.9803   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1553   -0.1553    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.3297   -0.8227    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0059   -1.5764    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.8264   -1.6626    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4790   -2.2438    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1435   -2.9975    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2995   -2.1576    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0997    0.6294    0.0000 N   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  1  1  0  0  0
  6  7  1  0  0  0  0
  7  8  1  6  0  0  0
  7  9  1  0  0  0  0
  9 10  2  0  0  0  0
  9 11  1  0  0  0  0
  5 12  1  0  0  0  0
  2 12  1  0  0  0  0
M  END
Download

3D MOL for NP0178200 (enduracididine)

     RDKit          3D

 24 24  0  0  0  0  0  0  0  0999 V2000
   -4.8810    0.4268    0.2956 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0425    1.0273    0.2198 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8735    0.4894    0.1823 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5808   -0.9080    0.2356 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1671   -1.0228   -0.0795 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6159    0.2705    0.4578 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.6730    0.6784   -0.1926 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7677   -0.3487   -0.0040 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.0292   -0.5400    1.3998 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.9927    0.0989   -0.7162 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0856    0.2715   -0.1227 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9519    0.3393   -2.0761 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6449    1.2166    0.0787 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2873   -1.6283    0.4602 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0991   -1.0745   -1.1846 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7232   -1.9190    0.3625 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4954    0.1837    1.5397 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5679    0.9428   -1.2513 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0210    1.6011    0.3314 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4850   -1.3336   -0.4436 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3776    0.3794    1.7904 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7758   -1.2350    1.5498 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2417   -0.1276   -2.6213 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5585    2.2118   -0.2115 H   0  0  0  0  0  0  0  0  0  0  0  0
  9  8  1  0
  8  7  1  0
  7  6  1  0
  6  5  1  0
  5  4  1  0
  4  3  1  0
  3  2  2  0
  3 13  1  0
  8 10  1  0
 10 12  1  0
 10 11  2  0
 13  6  1  0
  9 21  1  0
  9 22  1  0
  8 20  1  6
  7 18  1  0
  7 19  1  0
  6 17  1  1
  5 15  1  0
  5 16  1  0
  4 14  1  0
  2  1  1  0
 13 24  1  0
 12 23  1  0
M  END
Download

3D SDF for NP0178200 (enduracididine)


  Mrv1652309032218092D          

 12 12  0  0  1  0            999 V2000
    0.5678    1.9393    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.1143    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2352    0.6294    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.9803   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1553   -0.1553    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.3297   -0.8227    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0059   -1.5764    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.8264   -1.6626    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4790   -2.2438    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1435   -2.9975    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2995   -2.1576    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0997    0.6294    0.0000 N   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  1  1  0  0  0
  6  7  1  0  0  0  0
  7  8  1  6  0  0  0
  7  9  1  0  0  0  0
  9 10  2  0  0  0  0
  9 11  1  0  0  0  0
  5 12  1  0  0  0  0
  2 12  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0178200

> <DATABASE_NAME>
NP-MRD

> <SMILES>
N[C@@H](C[C@@H]1CNC(=N)N1)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C6H12N4O2/c7-4(5(11)12)1-3-2-9-6(8)10-3/h3-4H,1-2,7H2,(H,11,12)(H3,8,9,10)/t3-,4+/m1/s1

> <INCHI_KEY>
VFXRPXBQCNHQRQ-DMTCNVIQSA-N

> <FORMULA>
C6H12N4O2

> <MOLECULAR_WEIGHT>
172.188

> <EXACT_MASS>
172.096025642

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
24

> <JCHEM_AVERAGE_POLARIZABILITY>
16.66673654805721

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S)-2-amino-3-[(4R)-2-iminoimidazolidin-4-yl]propanoic acid

> <JCHEM_LOGP>
-3.5001624589376497

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.188637816187036

> <JCHEM_PKA_STRONGEST_BASIC>
11.981877859069565

> <JCHEM_POLAR_SURFACE_AREA>
111.23

> <JCHEM_REFRACTIVITY>
51.7543

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(2S)-2-amino-3-[(4R)-2-iminoimidazolidin-4-yl]propanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0178200 (enduracididine)

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PDB for NP0178200 (enduracididine)
HEADER    PROTEIN                                 03-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   03-SEP-22         0                                  
HETATM    1  N   UNK     0       1.060   3.620   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0       1.060   2.080   0.000  0.00  0.00           C+0
HETATM    3  N   UNK     0       2.306   1.175   0.000  0.00  0.00           N+0
HETATM    4  C   UNK     0       1.830  -0.290   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.290  -0.290   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -0.615  -1.536   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.011  -2.943   0.000  0.00  0.00           C+0
HETATM    8  N   UNK     0       1.543  -3.104   0.000  0.00  0.00           N+0
HETATM    9  C   UNK     0      -0.894  -4.188   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      -0.268  -5.595   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0      -2.426  -4.027   0.000  0.00  0.00           O+0
HETATM   12  N   UNK     0      -0.186   1.175   0.000  0.00  0.00           N+0
CONECT    1    2                                                            
CONECT    2    1    3   12                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6   12                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9                                                            
CONECT   12    5    2                                                       
MASTER        0    0    0    0    0    0    0    0   12    0   24    0
END

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3D PDB for NP0178200 (enduracididine)
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SMILES for NP0178200 (enduracididine)
N[C@@H](C[C@@H]1CNC(=N)N1)C(O)=O
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INCHI for NP0178200 (enduracididine)
InChI=1S/C6H12N4O2/c7-4(5(11)12)1-3-2-9-6(8)10-3/h3-4H,1-2,7H2,(H,11,12)(H3,8,9,10)/t3-,4+/m1/s1
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View in JSmol
Synonyms
ValueSource
L-Allo-enduracididineMeSH
L-End compoundMeSH
Chemical FormulaC6H12N4O2
Average Mass172.1880 Da
Monoisotopic Mass172.09603 Da
IUPAC NameNot Available
Traditional NameNot Available
CAS Registry NumberNot Available
SMILES
N[C@@H](C[C@@H]1CNC(=N)N1)C(O)=O
InChI Identifier
InChI=1S/C6H12N4O2/c7-4(5(11)12)1-3-2-9-6(8)10-3/h3-4H,1-2,7H2,(H,11,12)(H3,8,9,10)/t3-,4+/m1/s1
InChI KeyVFXRPXBQCNHQRQ-DMTCNVIQSA-N
Experimental Spectra
Not Available
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
Not Available
Species
Species of Origin
Species NameSourceReference
Streptomyces wadayamensisLOTUS Database
Chemical Taxonomy
Description Belongs to the class of organic compounds known as l-alpha-amino acids. These are alpha amino acids which have the L-configuration of the alpha-carbon atom.
KingdomOrganic compounds  
Super ClassOrganic acids and derivatives  
ClassCarboxylic acids and derivatives  
Sub ClassAmino acids, peptides, and analogues  
Direct ParentL-alpha-amino acids  
Alternative Parents
Substituents
  • L-alpha-amino acid
    • 

  • Imidazolyl carboxylic acid derivative
    • 

  • 2-imidazoline
    • 

  • Guanidine
    • 

  • Amino acid
    • 

  • Carboxylic acid
    • 

  • Monocarboxylic acid or derivatives
    • 

  • Carboximidamide
    • 

  • Propargyl-type 1,3-dipolar organic compound
    • 

  • Organic 1,3-dipolar compound
    • 

  • Organoheterocyclic compound
    • 

  • Azacycle
    • 

  • Primary amine
    • 

  • Organooxygen compound
    • 

  • Organonitrogen compound
    • 

  • Amine
    • 

  • Primary aliphatic amine
    • 

  • Carbonyl group
    • 

  • Organic nitrogen compound
    • 

  • Organic oxygen compound
    • 

  • Organopnictogen compound
    • 

  • Organic oxide
    • 

  • Hydrocarbon derivative
    • 

  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic 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
HMDB IDNot Available
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID24775830  
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkEnduracididine  
METLIN IDNot Available
PubChem Compound15284838  
PDB IDNot Available
ChEBI ID73969  
Good Scents IDNot Available
References
General References
  1. Han L, Vuksanovic N, Oehm SA, Fenske TG, Schwabacher AW, Silvaggi NR: Streptomyces wadayamensis MppP is a PLP-Dependent Oxidase, Not an Oxygenase. Biochemistry. 2018 Jun 12;57(23):3252-3264. doi: 10.1021/acs.biochem.8b00130. Epub 2018 Mar 6. [PubMed:29473729  ] 
  2. Han L, Schwabacher AW, Moran GR, Silvaggi NR: Streptomyces wadayamensis MppP Is a Pyridoxal 5'-Phosphate-Dependent L-Arginine alpha-Deaminase, gamma-Hydroxylase in the Enduracididine Biosynthetic Pathway. Biochemistry. 2015 Dec 1;54(47):7029-40. doi: 10.1021/acs.biochem.5b01016. Epub 2015 Nov 17. [PubMed:26551990  ] 
  3. Haltli B, Tan Y, Magarvey NA, Wagenaar M, Yin X, Greenstein M, Hucul JA, Zabriskie TM: Investigating beta-hydroxyenduracididine formation in the biosynthesis of the mannopeptimycins. Chem Biol. 2005 Nov;12(11):1163-8. doi: 10.1016/j.chembiol.2005.09.013. [PubMed:16298295  ] 
  4. LOTUS database [Link]