NP-MRD: Showing NP-Card for O2'-4alpha-cyclic-tetrahydrobiopterin (NP0339157)

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Record Information

Version

2.0

Created at

2024-09-11 19:57:48 UTC

Updated at

2024-09-11 19:57:48 UTC

NP-MRD ID

NP0339157

Secondary Accession Numbers

None

Natural Product Identification

Common Name

O2'-4alpha-cyclic-tetrahydrobiopterin

Description

11'-Carboxy-alpha-chromanol belongs to the class of organic compounds known as sesquiterpenoids. These are terpenes with three consecutive isoprene units. 11'-Carboxy-alpha-chromanol is an extremely weak basic (essentially neutral) compound (based on its pKa). Other major products of a-tocopherol oxidation include α-tocopherylquinone and epoxy-a-tocopherols. In addition to these oxidation products, the other major class of tocopherol metabolites is the carboxyethyl-hydroxychromans. The tocopherols ( a-tocopherol , b-tocopherol ,r-tocopherol and d-tocopherol ) and their corresponding tocotrienols are synthesized by plants and have vitamin E antixoidant activity (see pathway vitamin E biosynthesis ).

Structure

MOL SDF PDB SMILES InChI


  Mrv1652303102016492D          

 17 19  0  0  1  0            999 V2000
   12.6043  -16.8466    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.9200  -17.6088    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   13.7450  -17.6088    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   14.3283  -18.1922    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.1035  -18.2751    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   12.3366  -19.0172    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.9200  -19.6005    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.7450  -19.6005    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   14.3283  -19.0172    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.0428  -19.4297    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   15.7573  -19.0172    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.4718  -19.4297    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   15.7573  -18.1922    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   15.0428  -17.7797    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.0428  -16.9547    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.3366  -18.1922    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   11.5744  -17.8764    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  1  0  0  0
  2  3  1  0  0  0  0
  2 16  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  4  9  1  0  0  0  0
  4 14  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  6 16  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 11 13  2  0  0  0  0
 13 14  1  0  0  0  0
 14 15  2  0  0  0  0
 16 17  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0339157

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@H]1OC23NC(CNC2=NC(N)=NC3=O)[C@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C9H13N5O3/c1-3-5(15)4-2-11-6-9(14-4,17-3)7(16)13-8(10)12-6/h3-5,14-15H,2H2,1H3,(H3,10,11,12,13,16)/t3-,4?,5+,9?/m1/s1

> <INCHI_KEY>
JZTDUNXDDUJXRZ-UPYOWCHBSA-N

> <FORMULA>
C9H13N5O3

> <MOLECULAR_WEIGHT>
239.2312

> <EXACT_MASS>
239.101839307

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_ATOM_COUNT>
30

> <JCHEM_AVERAGE_POLARIZABILITY>
22.177499364697425

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(10R,11R)-4-amino-10-hydroxy-11-methyl-12-oxa-3,5,7,13-tetraazatricyclo[7.3.1.0^{1,6}]trideca-3,5-dien-2-one

> <ALOGPS_LOGP>
-1.67

> <JCHEM_LOGP>
-1.9725548943333333

> <ALOGPS_LOGS>
-1.59

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
18.23189706545675

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.568547752460386

> <JCHEM_PKA_STRONGEST_BASIC>
3.0128319424798145

> <JCHEM_POLAR_SURFACE_AREA>
121.33

> <JCHEM_REFRACTIVITY>
55.0852

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.17e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(10R,11R)-4-amino-10-hydroxy-11-methyl-12-oxa-3,5,7,13-tetraazatricyclo[7.3.1.0^{1,6}]trideca-3,5-dien-2-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 10-MAR-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   10-MAR-20         0                                  
HETATM    1  C   UNK     0      23.528 -31.447   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      24.117 -32.870   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0      25.657 -32.870   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0      26.746 -33.959   0.000  0.00  0.00           C+0
HETATM    5  N   UNK     0      24.460 -34.114   0.000  0.00  0.00           N+0
HETATM    6  C   UNK     0      23.028 -35.499   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      24.117 -36.588   0.000  0.00  0.00           C+0
HETATM    8  N   UNK     0      25.657 -36.588   0.000  0.00  0.00           N+0
HETATM    9  C   UNK     0      26.746 -35.499   0.000  0.00  0.00           C+0
HETATM   10  N   UNK     0      28.080 -36.269   0.000  0.00  0.00           N+0
HETATM   11  C   UNK     0      29.414 -35.499   0.000  0.00  0.00           C+0
HETATM   12  N   UNK     0      30.747 -36.269   0.000  0.00  0.00           N+0
HETATM   13  N   UNK     0      29.414 -33.959   0.000  0.00  0.00           N+0
HETATM   14  C   UNK     0      28.080 -33.189   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0      28.080 -31.649   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0      23.028 -33.959   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0      21.606 -33.369   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   16                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5    9   14                                             
CONECT    5    4    6                                                       
CONECT    6    5    7   16                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    4    8   10                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11   14                                                       
CONECT   14    4   13   15                                                  
CONECT   15   14                                                            
CONECT   16    2    6   17                                                  
CONECT   17   16                                                            
MASTER        0    0    0    0    0    0    0    0   17    0   38    0
END

View in JSmol

Synonyms

Value	Source
11'-Carboxy-alpha-tocopherol	HMDB
4a-Cyc-BH(,4)	HMDB
4a-Cyclic-tetrahydrobiopterin	HMDB

Chemical Formula

C₉H₁₃N₅O₃

Average Mass

239.2312 Da

Monoisotopic Mass

239.10184 Da

IUPAC Name

(10R,11R)-4-amino-10-hydroxy-11-methyl-12-oxa-3,5,7,13-tetraazatricyclo[7.3.1.0^{1,6}]trideca-3,5-dien-2-one

Traditional Name

(10R,11R)-4-amino-10-hydroxy-11-methyl-12-oxa-3,5,7,13-tetraazatricyclo[7.3.1.0^{1,6}]trideca-3,5-dien-2-one

CAS Registry Number

Not Available

SMILES

C[C@H]1OC23NC(CNC2=NC(N)=NC3=O)[C@H]1O

InChI Identifier

InChI=1S/C9H13N5O3/c1-3-5(15)4-2-11-6-9(14-4,17-3)7(16)13-8(10)12-6/h3-5,14-15H,2H2,1H3,(H3,10,11,12,13,16)/t3-,4?,5+,9?/m1/s1

InChI Key

JZTDUNXDDUJXRZ-UPYOWCHBSA-N

Experimental Spectra

Not Available

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Not Available

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as sesquiterpenoids. These are terpenes with three consecutive isoprene units.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Sesquiterpenoids

Direct Parent

Sesquiterpenoids

Alternative Parents

Substituents

Sesquiterpenoid
Long-chain fatty acid
Chromane
Benzopyran
1-benzopyran
Alkyl aryl ether
Branched fatty acid
Heterocyclic fatty acid
Methyl-branched fatty acid
Hydroxy fatty acid
Fatty acyl
Fatty acid
Benzenoid
Oxacycle
Carboxylic acid derivative
Carboxylic acid
Ether
Organoheterocyclic compound
Monocarboxylic acid or derivatives
Organic oxide
Hydrocarbon derivative
Organic oxygen compound
Organooxygen compound
Carbonyl group
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

Not Available

Physical Properties

State

Not Available

Experimental Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Predicted Properties

Property	Value	Source
logP	-1.7	ALOGPS
logP	-2	ChemAxon
logS	-1.6	ALOGPS
pKa (Strongest Acidic)	13.57	ChemAxon
pKa (Strongest Basic)	3.01	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	8	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	121.33 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	55.09 m³·mol⁻¹	ChemAxon
Polarizability	22.18 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

HMDB ID

HMDB0012515

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB029108

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

53481451

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Showing NP-Card for O2'-4alpha-cyclic-tetrahydrobiopterin (NP0339157)

MOL for NP0339157 (O2'-4alpha-cyclic-tetrahydrobiopterin)

3D MOL for NP0339157 (O2'-4alpha-cyclic-tetrahydrobiopterin)

3D SDF for NP0339157 (O2'-4alpha-cyclic-tetrahydrobiopterin)

3D-SDF for NP0339157 (O2'-4alpha-cyclic-tetrahydrobiopterin)

PDB for NP0339157 (O2'-4alpha-cyclic-tetrahydrobiopterin)

3D PDB for NP0339157 (O2'-4alpha-cyclic-tetrahydrobiopterin)

SMILES for NP0339157 (O2'-4alpha-cyclic-tetrahydrobiopterin)

INCHI for NP0339157 (O2'-4alpha-cyclic-tetrahydrobiopterin)

Structure for NP0339157 (O2'-4alpha-cyclic-tetrahydrobiopterin)

3D Structure for NP0339157 (O2'-4alpha-cyclic-tetrahydrobiopterin)