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Showing NP-Card for Coenzyme B (NP0340134)

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Record Information
Version2.0
Created at2024-09-12 01:41:14 UTC
Updated at2024-09-12 01:41:15 UTC
NP-MRD IDNP0340134
Secondary Accession NumbersNone
Natural Product Identification
Common NameCoenzyme B
DescriptionCoenzyme B belongs to the class of organic compounds known as n-acyl-alpha amino acids. N-acyl-alpha amino acids are compounds containing an alpha amino acid which bears an acyl group at its terminal nitrogen atom. Coenzyme B was first documented in 2024 (PMID: 38922714). Based on a literature review a small amount of articles have been published on Coenzyme B (PMID: 38914925) (PMID: 38548733) (PMID: 38464968) (PMID: 38416546).
Structure
Thumb
MOLSDFPDBSMILESInChI

MOL for NP0340134 (Coenzyme B)


  Mrv2104 05272304132D          

 21 20  0  0  0  0            999 V2000
    6.5408   -0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2539    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5395    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9684    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6829    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1105    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.5408    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3974    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8263    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8263    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1118    0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.3974    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.1118    1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.5408    1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.6842   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.3822    0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.5572   -0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.2552    0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.9697    0.0000    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6039    0.0000    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
  3  2  1  0  0  0  0
  4  2  1  0  0  0  0
  5  3  1  0  0  0  0
  6  4  1  0  0  0  0
  7  5  1  0  0  0  0
  8  1  1  0  0  0  0
  9  6  1  0  0  0  0
 10  8  1  0  0  0  0
 11 10  1  0  0  0  0
 12  9  2  0  0  0  0
 12 10  1  4  0  0  0
 13  9  1  0  0  0  0
 14 11  2  0  0  0  0
 15 11  1  0  0  0  0
 19  8  1  0  0  0  0
 20 16  1  0  0  0  0
 20 17  1  0  0  0  0
 20 18  2  0  0  0  0
 20 19  1  0  0  0  0
 21  7  1  0  0  0  0
M  END
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3D MOL for NP0340134 (Coenzyme B)

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3D SDF for NP0340134 (Coenzyme B)

  Mrv2104 05272304132D          

 21 20  0  0  0  0            999 V2000
    6.5408   -0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2539    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5395    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9684    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6829    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1105    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.5408    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3974    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8263    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8263    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1118    0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.3974    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.1118    1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.5408    1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.6842   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.3822    0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.5572   -0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.2552    0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.9697    0.0000    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6039    0.0000    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
  3  2  1  0  0  0  0
  4  2  1  0  0  0  0
  5  3  1  0  0  0  0
  6  4  1  0  0  0  0
  7  5  1  0  0  0  0
  8  1  1  0  0  0  0
  9  6  1  0  0  0  0
 10  8  1  0  0  0  0
 11 10  1  0  0  0  0
 12  9  2  0  0  0  0
 12 10  1  4  0  0  0
 13  9  1  0  0  0  0
 14 11  2  0  0  0  0
 15 11  1  0  0  0  0
 19  8  1  0  0  0  0
 20 16  1  0  0  0  0
 20 17  1  0  0  0  0
 20 18  2  0  0  0  0
 20 19  1  0  0  0  0
 21  7  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0340134

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(OP(O)(O)=O)C(N=C(O)CCCCCCS)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1/C11H22NO7PS/c1-8(19-20(16,17)18)10(11(14)15)12-9(13)6-4-2-3-5-7-21/h8,10,21H,2-7H2,1H3,(H,12,13)(H,14,15)(H2,16,17,18)

> <INCHI_KEY>
JBJSVEVEEGOEBZ-UHFFFAOYNA-N

> <FORMULA>
C11H22NO7PS

> <MOLECULAR_WEIGHT>
343.33

> <EXACT_MASS>
343.085460224

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
43

> <JCHEM_AVERAGE_POLARIZABILITY>
33.271356759002416

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
2-[(1-hydroxy-7-sulfanylheptylidene)amino]-3-(phosphonooxy)butanoic acid

> <JCHEM_LOGP>
1.2390144692481284

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-3

> <JCHEM_PKA>
3.9018975137203884

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.2915695266794331

> <JCHEM_PKA_STRONGEST_BASIC>
0.3718179882366659

> <JCHEM_POLAR_SURFACE_AREA>
136.65

> <JCHEM_REFRACTIVITY>
78.28639999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
11

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
2-[(1-hydroxy-7-sulfanylheptylidene)amino]-3-(phosphonooxy)butanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$

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3D-SDF for NP0340134 (Coenzyme B)
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PDB for NP0340134 (Coenzyme B)
HEADER    PROTEIN                                 27-MAY-23   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   27-MAY-23         0                                  
HETATM    1  C   UNK     0      12.209  -1.540   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       4.207   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.874   0.770   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       5.541   0.770   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.540   0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       6.875   0.000   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.206   0.770   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      12.209   0.000   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       8.208   0.770   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      10.876   0.770   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      10.876   2.310   0.000  0.00  0.00           C+0
HETATM   12  N   UNK     0       9.542   0.000   0.000  0.00  0.00           N+0
HETATM   13  O   UNK     0       8.208   2.310   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0       9.542   3.080   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0      12.209   3.080   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0      16.211  -0.770   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0      15.647   1.334   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0      14.107  -1.334   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0      13.543   0.770   0.000  0.00  0.00           O+0
HETATM   20  P   UNK     0      14.877   0.000   0.000  0.00  0.00           P+0
HETATM   21  S   UNK     0      -1.127   0.000   0.000  0.00  0.00           S+0
CONECT    1    8                                                            
CONECT    2    3    4                                                       
CONECT    3    2    5                                                       
CONECT    4    2    6                                                       
CONECT    5    3    7                                                       
CONECT    6    4    9                                                       
CONECT    7    5   21                                                       
CONECT    8    1   10   19                                                  
CONECT    9    6   12   13                                                  
CONECT   10    8   11   12                                                  
CONECT   11   10   14   15                                                  
CONECT   12    9   10                                                       
CONECT   13    9                                                            
CONECT   14   11                                                            
CONECT   15   11                                                            
CONECT   16   20                                                            
CONECT   17   20                                                            
CONECT   18   20                                                            
CONECT   19    8   20                                                       
CONECT   20   16   17   18   19                                             
CONECT   21    7                                                            
MASTER        0    0    0    0    0    0    0    0   21    0   40    0
END

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3D PDB for NP0340134 (Coenzyme B)
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SMILES for NP0340134 (Coenzyme B)
CC(OP(O)(O)=O)C(N=C(O)CCCCCCS)C(O)=O
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INCHI for NP0340134 (Coenzyme B)
InChI=1/C11H22NO7PS/c1-8(19-20(16,17)18)10(11(14)15)12-9(13)6-4-2-3-5-7-21/h8,10,21H,2-7H2,1H3,(H,12,13)(H,14,15)(H2,16,17,18)
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View in JSmol
SynonymsNot Available
Chemical FormulaC11H22NO7PS
Average Mass343.3300 Da
Monoisotopic Mass343.08546 Da
IUPAC Name2-[(1-hydroxy-7-sulfanylheptylidene)amino]-3-(phosphonooxy)butanoic acid
Traditional Name2-[(1-hydroxy-7-sulfanylheptylidene)amino]-3-(phosphonooxy)butanoic acid
CAS Registry NumberNot Available
SMILES
CC(OP(O)(O)=O)C(N=C(O)CCCCCCS)C(O)=O
InChI Identifier
InChI=1/C11H22NO7PS/c1-8(19-20(16,17)18)10(11(14)15)12-9(13)6-4-2-3-5-7-21/h8,10,21H,2-7H2,1H3,(H,12,13)(H,14,15)(H2,16,17,18)
InChI KeyJBJSVEVEEGOEBZ-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 n-acyl-alpha amino acids. These are compounds containing an alpha amino acid which bears an acyl group at its terminal nitrogen atom.
KingdomOrganic compounds  
Super ClassOrganic acids and derivatives  
ClassCarboxylic acids and derivatives  
Sub ClassAmino acids, peptides, and analogues  
Direct ParentN-acyl-alpha amino acids  
Alternative Parents
Substituents
  • N-acyl-alpha-amino acid
    • 

  • Phosphoethanolamine
    • 

  • Monoalkyl phosphate
    • 

  • Fatty amide
    • 

  • N-acyl-amine
    • 

  • Organic phosphoric acid derivative
    • 

  • Fatty acyl
    • 

  • Fatty acid
    • 

  • Alkyl phosphate
    • 

  • Phosphoric acid ester
    • 

  • Carboxamide group
    • 

  • Secondary carboxylic acid amide
    • 

  • Alkylthiol
    • 

  • Carboxylic acid
    • 

  • Monocarboxylic acid or derivatives
    • 

  • Hydrocarbon derivative
    • 

  • Organic oxide
    • 

  • Organopnictogen compound
    • 

  • Carbonyl group
    • 

  • Organic oxygen compound
    • 

  • Organic nitrogen compound
    • 

  • Organonitrogen compound
    • 

  • Organooxygen compound
    • 

  • Organosulfur compound
    • 

  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External DescriptorsNot Available
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
logP1.24ChemAxon
pKa (Strongest Acidic)1.29ChemAxon
pKa (Strongest Basic)0.37ChemAxon
Physiological Charge-3ChemAxon
Hydrogen Acceptor Count7ChemAxon
Hydrogen Donor Count5ChemAxon
Polar Surface Area136.65 ŲChemAxon
Rotatable Bond Count11ChemAxon
Refractivity78.29 m³·mol⁻¹ChemAxon
Polarizability33.27 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
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 LinkCoenzyme B  
METLIN IDNot Available
PubChem CompoundNot Available
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. Musiari A, Reichenbach M, Gallo S, Sigel RKO: Corrin Ring Modifications Reveal the Chemical and Spatial Requirements for the B(12)-btuB Riboswitch Interaction. Chemistry. 2024 Sep 2;30(49):e202401800. doi: 10.1002/chem.202401800. Epub 2024  Aug 13. [PubMed:38922714  ] 
  2. Poleto MD, Allen KD, Lemkul JA: Structural Dynamics of the Methyl-Coenzyme M Reductase Active Site Are Influenced by Coenzyme F(430) Modifications. Biochemistry. 2024 Jul 16;63(14):1783-1794. doi: 10.1021/acs.biochem.4c00168.  Epub 2024 Jun 24. [PubMed:38914925  ] 
  3. Zhang S, Jeffreys LN, Poddar H, Yu Y, Liu C, Patel K, Johannissen LO, Zhu L, Cliff MJ, Yan C, Schiro G, Weik M, Sakuma M, Levy CW, Leys D, Heyes DJ, Scrutton NS: Photocobilins integrate B(12) and bilin photochemistry for enzyme control. Nat Commun. 2024 Mar 28;15(1):2740. doi: 10.1038/s41467-024-46995-1. [PubMed:38548733  ] 
  4. Lazar L, Eshel A, Moadi L, Yackobovitch-Gavan M, Bar-Maisels M, Shtaif B, Nevo M, Phillip M, Turjeman S, Koren O, Gat-Yablonski G: Children with idiopathic short stature have significantly different gut microbiota than their normal height siblings: a case-control study. Front Endocrinol (Lausanne). 2024 Feb 23;15:1343337. doi:  10.3389/fendo.2024.1343337. eCollection 2024. [PubMed:38464968  ] 
  5. Perez-Castano R, Aranda J, Widner FJ, Kieninger C, Deery E, Warren MJ, Orozco M, Elias-Arnanz M, Padmanabhan S, Krautler B: The Rhodium Analogue of Coenzyme B(12) as an Anti-Photoregulatory Ligand Inhibiting Bacterial CarH Photoreceptors. Angew Chem Int Ed Engl. 2024 Apr 24;63(18):e202401626. doi:  10.1002/anie.202401626. Epub 2024 Mar 19. [PubMed:38416546  ]