NP-MRD: Showing NP-Card for 4-Oxo-13-cis-retinoate (NP0339091)

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Record Information

Version

2.0

Created at

2024-09-11 19:38:30 UTC

Updated at

2024-09-11 19:38:30 UTC

NP-MRD ID

NP0339091

Secondary Accession Numbers

None

Natural Product Identification

Common Name

4-Oxo-13-cis-retinoate

Description

4-Oxo-13-cis-retinoate, also known as 4O13CVA, belongs to the class of organic compounds known as retinoids. These are oxygenated derivatives of 3,7-dimethyl-1-(2,6,6-trimethylcyclohex-1-enyl)nona-1,3,5,7-tetraene and derivatives thereof. 4-Oxo-13-cis-retinoate is an extremely weak basic (essentially neutral) compound (based on its pKa). While the 4-oxo metabolite is less potent than the parent compound.

Structure

MOL SDF PDB SMILES InChI


  Mrv0541 02251208092D          

 23 23  0  0  0  0            999 V2000
   11.4030  -12.9920    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.9906  -12.2774    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.4030  -11.5629    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.2279  -11.5629    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.6404  -10.8484    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.4654  -10.8484    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.8778  -11.5629    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.8778  -10.1338    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.7021  -10.1338    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.1146  -10.8484    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.9395  -10.8490    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.3520  -11.5635    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.3526  -10.1351    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.9414   -9.4200    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.3563   -8.7066    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.1171   -9.4181    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.9906  -10.8484    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.7051  -10.4359    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.9906  -10.0234    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.1656  -10.8484    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.7531  -10.1338    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.7531  -11.5629    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.1656  -12.2774    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  2 23  1  0  0  0  0
  3  4  1  0  0  0  0
  3 17  1  0  0  0  0
  4  5  2  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  6  8  2  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  1  0  0  0  0
 14 16  2  0  0  0  0
 17 18  1  0  0  0  0
 17 19  1  0  0  0  0
 17 20  1  0  0  0  0
 20 21  2  0  0  0  0
 20 22  1  0  0  0  0
 22 23  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0339091

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C\C(\C=C\C1=C(C)CCC(=O)C1(C)C)=C/C=C/C(/C)=C\C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C20H26O3/c1-14(7-6-8-15(2)13-19(22)23)9-11-17-16(3)10-12-18(21)20(17,4)5/h6-9,11,13H,10,12H2,1-5H3,(H,22,23)/b8-6+,11-9+,14-7+,15-13-

> <INCHI_KEY>
YOFBBAJVETYSCH-IWRFDTMXSA-N

> <FORMULA>
C20H26O3

> <MOLECULAR_WEIGHT>
314.4186

> <EXACT_MASS>
314.188194698

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_AVERAGE_POLARIZABILITY>
36.57001801548519

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(2Z,4E,6E,8E)-3,7-dimethyl-9-(2,6,6-trimethyl-5-oxocyclohex-1-en-1-yl)nona-2,4,6,8-tetraenoic acid

> <ALOGPS_LOGP>
4.83

> <JCHEM_LOGP>
4.347084349666667

> <ALOGPS_LOGS>
-4.75

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
19.83826678221873

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.9966477449975715

> <JCHEM_PKA_STRONGEST_BASIC>
-7.559579122554959

> <JCHEM_POLAR_SURFACE_AREA>
54.37

> <JCHEM_REFRACTIVITY>
98.48399999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.60e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2Z,4E,6E,8E)-3,7-dimethyl-9-(2,6,6-trimethyl-5-oxocyclohex-1-en-1-yl)nona-2,4,6,8-tetraenoic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 25-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   25-FEB-12         0                                  
HETATM    1  C   UNK     0      21.286 -24.252   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      20.516 -22.918   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      21.286 -21.584   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      22.825 -21.584   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      23.595 -20.250   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      25.135 -20.250   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      25.905 -21.584   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      25.905 -18.916   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      27.444 -18.916   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      28.214 -20.250   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      29.754 -20.251   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      30.524 -21.585   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      30.525 -18.919   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      29.757 -17.584   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0      30.532 -16.252   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0      28.219 -17.580   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0      20.516 -20.250   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      21.850 -19.480   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      20.516 -18.710   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      18.976 -20.250   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0      18.206 -18.916   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0      18.206 -21.584   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      18.976 -22.918   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3   23                                                  
CONECT    3    2    4   17                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11   14                                                       
CONECT   14   13   15   16                                                  
CONECT   15   14                                                            
CONECT   16   14                                                            
CONECT   17    3   18   19   20                                             
CONECT   18   17                                                            
CONECT   19   17                                                            
CONECT   20   17   21   22                                                  
CONECT   21   20                                                            
CONECT   22   20   23                                                       
CONECT   23    2   22                                                       
MASTER        0    0    0    0    0    0    0    0   23    0   46    0
END

View in JSmol

Synonyms

Value	Source
4-oxo-13-cis-Retinoic acid	Generator
3,7-Dimethyl-9-(5-oxo-2,6,6-trimethyl-1-cyclohexenyl)-(2E,4Z,6Z,8Z)-nonatetraen-1-Oate	HMDB
3,7-Dimethyl-9-(5-oxo-2,6,6-trimethyl-1-cyclohexenyl)-(2E,4Z,6Z,8Z)-nonatetraen-1-Oic acid	HMDB
4-Keto-13-cis-retinoate	HMDB
4-Keto-13-cis-retinoic acid	HMDB
4-oxo-13-cis-Retinoic acid anion	HMDB
4O13CVA	HMDB
(2Z,4E,6E,8E)-3,7-Dimethyl-9-(2,6,6-trimethyl-5-oxocyclohex-1-en-1-yl)nona-2,4,6,8-tetraenoate	Generator

Chemical Formula

C₂₀H₂₆O₃

Average Mass

314.4186 Da

Monoisotopic Mass

314.18819 Da

IUPAC Name

(2Z,4E,6E,8E)-3,7-dimethyl-9-(2,6,6-trimethyl-5-oxocyclohex-1-en-1-yl)nona-2,4,6,8-tetraenoic acid

Traditional Name

(2Z,4E,6E,8E)-3,7-dimethyl-9-(2,6,6-trimethyl-5-oxocyclohex-1-en-1-yl)nona-2,4,6,8-tetraenoic acid

CAS Registry Number

Not Available

SMILES

C\C(\C=C\C1=C(C)CCC(=O)C1(C)C)=C/C=C/C(/C)=C\C(O)=O

InChI Identifier

InChI=1S/C20H26O3/c1-14(7-6-8-15(2)13-19(22)23)9-11-17-16(3)10-12-18(21)20(17,4)5/h6-9,11,13H,10,12H2,1-5H3,(H,22,23)/b8-6+,11-9+,14-7+,15-13-

InChI Key

YOFBBAJVETYSCH-IWRFDTMXSA-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 retinoids. These are oxygenated derivatives of 3,7-dimethyl-1-(2,6,6-trimethylcyclohex-1-enyl)nona-1,3,5,7-tetraene and derivatives thereof.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Retinoids

Direct Parent

Retinoids

Alternative Parents

Substituents

Retinoic acid
Diterpenoid
Retinoid skeleton
Medium-chain fatty acid
Cyclohexenone
Methyl-branched fatty acid
Branched fatty acid
Fatty acyl
Fatty acid
Unsaturated fatty acid
Ketone
Cyclic ketone
Monocarboxylic acid or derivatives
Carboxylic acid
Carboxylic acid derivative
Organooxygen compound
Organic oxide
Carbonyl group
Hydrocarbon derivative
Organic oxygen compound
Aliphatic homomonocyclic compound

Molecular Framework

Aliphatic homomonocyclic 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	4.83	ALOGPS
logP	4.35	ChemAxon
logS	-4.8	ALOGPS
pKa (Strongest Acidic)	5	ChemAxon
pKa (Strongest Basic)	-7.6	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	54.37 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	98.48 m³·mol⁻¹	ChemAxon
Polarizability	36.57 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

HMDB ID

HMDB0012789

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB029175

KNApSAcK ID

Not Available

Chemspider ID

8171361

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

9995780

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Showing NP-Card for 4-Oxo-13-cis-retinoate (NP0339091)

MOL for NP0339091 (4-Oxo-13-cis-retinoate)

3D MOL for NP0339091 (4-Oxo-13-cis-retinoate)

3D SDF for NP0339091 (4-Oxo-13-cis-retinoate)

3D-SDF for NP0339091 (4-Oxo-13-cis-retinoate)

PDB for NP0339091 (4-Oxo-13-cis-retinoate)

3D PDB for NP0339091 (4-Oxo-13-cis-retinoate)

SMILES for NP0339091 (4-Oxo-13-cis-retinoate)

INCHI for NP0339091 (4-Oxo-13-cis-retinoate)

Structure for NP0339091 (4-Oxo-13-cis-retinoate)

3D Structure for NP0339091 (4-Oxo-13-cis-retinoate)