NP-MRD: Showing NP-Card for 9,13-cis-Retinoate (NP0339107)

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Record Information

Version

2.0

Created at

2024-09-11 19:43:05 UTC

Updated at

2024-09-11 19:43:05 UTC

NP-MRD ID

NP0339107

Secondary Accession Numbers

None

Natural Product Identification

Common Name

9,13-cis-Retinoate

Description

9,13-Cis-Retinoic acid, also known as 9,13-cis-vitamin-a-acid or 9,13-di-cis-ra, 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. 9,13-Cis-Retinoic acid is a very hydrophobic molecule, practically insoluble (in water), and relatively neutral.

Structure

MOL SDF PDB SMILES InChI

6419708
  Mrv1652305281820312D          

 22 22  0  0  0  0            999 V2000
    8.8777   -1.7473    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.1633   -0.5099    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4474    1.1401    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7329    0.7276    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7329   -0.0973    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1618    0.7276    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4473   -0.5098    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1618   -0.0973    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0349    1.8546    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8599    1.8546    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8763    1.1401    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8764   -0.5098    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5908    0.7276    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3053    1.1401    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3053    1.9651    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0198    0.7276    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0198   -0.0973    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.7343   -0.5098    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.7343   -1.3349    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0198   -1.7474    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.4488   -1.7474    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.1633   -1.3349    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1 22  1  0  0  0  0
  2 22  2  0  0  0  0
  3  4  1  0  0  0  0
  3  6  1  0  0  0  0
  3  9  1  0  0  0  0
  3 10  1  0  0  0  0
  4  5  1  0  0  0  0
  5  7  1  0  0  0  0
  6  8  2  0  0  0  0
  6 11  1  0  0  0  0
  7  8  1  0  0  0  0
  8 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
 16 17  1  0  0  0  0
 17 18  2  0  0  0  0
 18 19  1  0  0  0  0
 19 20  1  0  0  0  0
 19 21  2  0  0  0  0
 21 22  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0339107

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C\C(\C=C\C1=C(C)CCCC1(C)C)=C\C=C\C(\C)=C/C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C20H28O2/c1-15(8-6-9-16(2)14-19(21)22)11-12-18-17(3)10-7-13-20(18,4)5/h6,8-9,11-12,14H,7,10,13H2,1-5H3,(H,21,22)/b9-6+,12-11+,15-8-,16-14-

> <INCHI_KEY>
SHGAZHPCJJPHSC-CDMOMSTLSA-N

> <FORMULA>
C20H28O2

> <MOLECULAR_WEIGHT>
300.4351

> <EXACT_MASS>
300.20893014

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
50

> <JCHEM_AVERAGE_POLARIZABILITY>
35.86837717218032

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

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

> <ALOGPS_LOGP>
5.66

> <JCHEM_LOGP>
5.014367711

> <ALOGPS_LOGS>
-4.80

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.996647744997455

> <JCHEM_POLAR_SURFACE_AREA>
37.3

> <JCHEM_REFRACTIVITY>
97.79079999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
4.77e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
9,13-di-cis-retinoic acid

> <JCHEM_VEBER_RULE>
1

$$$$

HEADER    PROTEIN                                 28-MAY-18   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: 6419708                                           
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   28-MAY-18         0                                  
HETATM    1  O   UNK     0      16.572  -3.262   0.000  0.00  0.00           O+0
HETATM    2  O   UNK     0      15.238  -0.952   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0       4.568   2.128   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       3.235   1.358   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       3.235  -0.182   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       5.902   1.358   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       4.568  -0.952   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       5.902  -0.182   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       3.798   3.462   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       5.338   3.462   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       7.236   2.128   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       7.236  -0.952   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       8.569   1.358   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       9.903   2.128   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       9.903   3.668   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      11.237   1.358   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      11.237  -0.182   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      12.571  -0.952   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      12.571  -2.492   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      11.237  -3.262   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      13.904  -3.262   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      15.238  -2.492   0.000  0.00  0.00           C+0
CONECT    1   22                                                            
CONECT    2   22                                                            
CONECT    3    4    6    9   10                                             
CONECT    4    3    5                                                       
CONECT    5    4    7                                                       
CONECT    6    3    8   11                                                  
CONECT    7    5    8                                                       
CONECT    8    6    7   12                                                  
CONECT    9    3                                                            
CONECT   10    3                                                            
CONECT   11    6   13                                                       
CONECT   12    8                                                            
CONECT   13   11   14                                                       
CONECT   14   13   15   16                                                  
CONECT   15   14                                                            
CONECT   16   14   17                                                       
CONECT   17   16   18                                                       
CONECT   18   17   19                                                       
CONECT   19   18   20   21                                                  
CONECT   20   19                                                            
CONECT   21   19   22                                                       
CONECT   22    1    2   21                                                  
MASTER        0    0    0    0    0    0    0    0   22    0   44    0
END

View in JSmol

Synonyms

Value	Source
9,13-cis-Retinoate	Generator
3,7-Dimethyl-9-(2,6,6-trimethyl-1-cyclohexenyl)-(2E,4Z,6E,8Z)-nonatetraen-1-Oate	HMDB
3,7-Dimethyl-9-(2,6,6-trimethyl-1-cyclohexenyl)-(2E,4Z,6E,8Z)-nonatetraen-1-Oic acid	HMDB
9,13-cis-Retinoic acid anion	HMDB
9,13-cis-Vitamin-a-acid	HMDB
9,13-cis-Vitamin-alpha-acid	HMDB
9,13-Di-cis-ra	HMDB
9-cis,13-cis-Retinoate	HMDB
9-cis,13-cis-Retinoic acid	HMDB
DcVA	HMDB
9,13-Retinoic acid	HMDB
9,13-cis-Retinoic acid	HMDB, Generator
9,13-Di-cis-retinoate	Generator

Chemical Formula

C₂₀H₂₈O₂

Average Mass

300.4351 Da

Monoisotopic Mass

300.20893 Da

IUPAC Name

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

Traditional Name

9,13-di-cis-retinoic acid

CAS Registry Number

Not Available

SMILES

C\C(\C=C\C1=C(C)CCCC1(C)C)=C\C=C\C(\C)=C/C(O)=O

InChI Identifier

InChI=1S/C20H28O2/c1-15(8-6-9-16(2)14-19(21)22)11-12-18-17(3)10-7-13-20(18,4)5/h6,8-9,11-12,14H,7,10,13H2,1-5H3,(H,21,22)/b9-6+,12-11+,15-8-,16-14-

InChI Key

SHGAZHPCJJPHSC-CDMOMSTLSA-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
Branched fatty acid
Methyl-branched fatty acid
Fatty acyl
Unsaturated fatty acid
Fatty acid
Monocarboxylic acid or derivatives
Carboxylic acid
Carboxylic acid derivative
Hydrocarbon derivative
Organooxygen compound
Organic oxide
Organic oxygen compound
Carbonyl group
Aliphatic homomonocyclic compound

Molecular Framework

Aliphatic homomonocyclic compounds

External Descriptors

Retinoids (LMPR01090023 )

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	5.66	ALOGPS
logP	5.01	ChemAxon
logS	-4.8	ALOGPS
pKa (Strongest Acidic)	5	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	2	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	37.3 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	97.79 m³·mol⁻¹	ChemAxon
Polarizability	35.87 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

HMDB ID

HMDB0012874

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB029194

KNApSAcK ID

Not Available

Chemspider ID

4925342

KEGG Compound ID

C00777

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

6419708

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Showing NP-Card for 9,13-cis-Retinoate (NP0339107)

MOL for NP0339107 (9,13-cis-Retinoate)

3D MOL for NP0339107 (9,13-cis-Retinoate)

3D SDF for NP0339107 (9,13-cis-Retinoate)

3D-SDF for NP0339107 (9,13-cis-Retinoate)

PDB for NP0339107 (9,13-cis-Retinoate)

3D PDB for NP0339107 (9,13-cis-Retinoate)

SMILES for NP0339107 (9,13-cis-Retinoate)

INCHI for NP0339107 (9,13-cis-Retinoate)

Structure for NP0339107 (9,13-cis-Retinoate)

3D Structure for NP0339107 (9,13-cis-Retinoate)