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Showing NP-Card for (4r,5r)-4-hydroxy-5-(2-hydroxyethyl)-2-(hydroxymethyl)cyclopent-1-ene-1-carboxylic acid (NP0243404)

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Record Information
Version2.0
Created at2022-09-07 03:56:41 UTC
Updated at2022-09-07 03:56:41 UTC
NP-MRD IDNP0243404
Secondary Accession NumbersNone
Natural Product Identification
Common Name(4r,5r)-4-hydroxy-5-(2-hydroxyethyl)-2-(hydroxymethyl)cyclopent-1-ene-1-carboxylic acid
DescriptionCrescentin II belongs to the class of organic compounds known as iridoids and derivatives. These are monoterpenes containing a skeleton structurally characterized by the presence of a cylopentane fused to a pyran ( forming a 4,7-dimethylcyclopenta[c]pyran), or a derivative where the pentane moiety is open. (4r,5r)-4-hydroxy-5-(2-hydroxyethyl)-2-(hydroxymethyl)cyclopent-1-ene-1-carboxylic acid is found in Crescentia cujete and Vitex rotundifolia. Based on a literature review very few articles have been published on Crescentin II.
Structure
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MOLSDFPDBSMILESInChI

MOL for NP0243404 ((4r,5r)-4-hydroxy-5-(2-hydroxyethyl)-2-(hydroxymethyl)cyclopent-1-ene-1-carboxylic acid)


  Mrv1652309072205562D          

 14 14  0  0  1  0            999 V2000
   -0.1467    2.3518    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.9393    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2822    2.3518    0.0000 O   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 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0198    0.8843    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6329    0.3323    0.0000 O   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 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0997    0.6294    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.8843    0.8843    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0558    1.6913    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8405    1.9462    0.0000 O   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
  2  4  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
  5  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  1  0  0  0
  9 11  1  0  0  0  0
  4 11  1  0  0  0  0
 11 12  1  6  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
M  END
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3D MOL for NP0243404 ((4r,5r)-4-hydroxy-5-(2-hydroxyethyl)-2-(hydroxymethyl)cyclopent-1-ene-1-carboxylic acid)

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3D SDF for NP0243404 ((4r,5r)-4-hydroxy-5-(2-hydroxyethyl)-2-(hydroxymethyl)cyclopent-1-ene-1-carboxylic acid)

  Mrv1652309072205562D          

 14 14  0  0  1  0            999 V2000
   -0.1467    2.3518    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.9393    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2822    2.3518    0.0000 O   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 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0198    0.8843    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6329    0.3323    0.0000 O   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 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0997    0.6294    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.8843    0.8843    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0558    1.6913    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8405    1.9462    0.0000 O   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
  2  4  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
  5  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  1  0  0  0
  9 11  1  0  0  0  0
  4 11  1  0  0  0  0
 11 12  1  6  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0243404

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OCC[C@H]1[C@H](O)CC(CO)=C1C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C9H14O5/c10-2-1-6-7(12)3-5(4-11)8(6)9(13)14/h6-7,10-12H,1-4H2,(H,13,14)/t6-,7+/m0/s1

> <INCHI_KEY>
HYJIDONKRRKLEJ-NKWVEPMBSA-N

> <FORMULA>
C9H14O5

> <MOLECULAR_WEIGHT>
202.206

> <EXACT_MASS>
202.084123551

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
28

> <JCHEM_AVERAGE_POLARIZABILITY>
19.89183042692409

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(4R,5R)-4-hydroxy-5-(2-hydroxyethyl)-2-(hydroxymethyl)cyclopent-1-ene-1-carboxylic acid

> <JCHEM_LOGP>
-1.7552899983333332

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
14.628014933046188

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.30389263407522

> <JCHEM_PKA_STRONGEST_BASIC>
-2.3835907956626308

> <JCHEM_POLAR_SURFACE_AREA>
97.99000000000001

> <JCHEM_REFRACTIVITY>
48.8483

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(4R,5R)-4-hydroxy-5-(2-hydroxyethyl)-2-(hydroxymethyl)cyclopent-1-ene-1-carboxylic acid

> <JCHEM_VEBER_RULE>
0

$$$$

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3D-SDF for NP0243404 ((4r,5r)-4-hydroxy-5-(2-hydroxyethyl)-2-(hydroxymethyl)cyclopent-1-ene-1-carboxylic acid)
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PDB for NP0243404 ((4r,5r)-4-hydroxy-5-(2-hydroxyethyl)-2-(hydroxymethyl)cyclopent-1-ene-1-carboxylic acid)
HEADER    PROTEIN                                 07-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   07-SEP-22         0                                  
HETATM    1  O   UNK     0      -0.274   4.390   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       1.060   3.620   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0       2.393   4.390   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0       1.060   2.080   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.306   1.175   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       3.770   1.651   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       4.915   0.620   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       1.830  -0.290   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       0.290  -0.290   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      -0.615  -1.536   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0      -0.186   1.175   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -1.651   1.651   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -1.971   3.157   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0      -3.436   3.633   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5   11                                                  
CONECT    5    4    6    8                                                  
CONECT    6    5    7                                                       
CONECT    7    6                                                            
CONECT    8    5    9                                                       
CONECT    9    8   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9    4   12                                                  
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13                                                            
MASTER        0    0    0    0    0    0    0    0   14    0   28    0
END

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3D PDB for NP0243404 ((4r,5r)-4-hydroxy-5-(2-hydroxyethyl)-2-(hydroxymethyl)cyclopent-1-ene-1-carboxylic acid)
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SMILES for NP0243404 ((4r,5r)-4-hydroxy-5-(2-hydroxyethyl)-2-(hydroxymethyl)cyclopent-1-ene-1-carboxylic acid)
OCC[C@H]1[C@H](O)CC(CO)=C1C(O)=O
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INCHI for NP0243404 ((4r,5r)-4-hydroxy-5-(2-hydroxyethyl)-2-(hydroxymethyl)cyclopent-1-ene-1-carboxylic acid)
InChI=1S/C9H14O5/c10-2-1-6-7(12)3-5(4-11)8(6)9(13)14/h6-7,10-12H,1-4H2,(H,13,14)/t6-,7+/m0/s1
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SynonymsNot Available
Chemical FormulaC9H14O5
Average Mass202.2060 Da
Monoisotopic Mass202.08412 Da
IUPAC Name(4R,5R)-4-hydroxy-5-(2-hydroxyethyl)-2-(hydroxymethyl)cyclopent-1-ene-1-carboxylic acid
Traditional Name(4R,5R)-4-hydroxy-5-(2-hydroxyethyl)-2-(hydroxymethyl)cyclopent-1-ene-1-carboxylic acid
CAS Registry NumberNot Available
SMILES
OCC[C@H]1[C@H](O)CC(CO)=C1C(O)=O
InChI Identifier
InChI=1S/C9H14O5/c10-2-1-6-7(12)3-5(4-11)8(6)9(13)14/h6-7,10-12H,1-4H2,(H,13,14)/t6-,7+/m0/s1
InChI KeyHYJIDONKRRKLEJ-NKWVEPMBSA-N
Experimental Spectra
Not Available
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Crescentia cujeteLOTUS Database
Vitex rotundifoliaLOTUS Database
Chemical Taxonomy
Description Belongs to the class of organic compounds known as iridoids and derivatives. These are monoterpenes containing a skeleton structurally characterized by the presence of a cylopentane fused to a pyran ( forming a 4,7-dimethylcyclopenta[c]pyran), or a derivative where the pentane moiety is open.
KingdomOrganic compounds  
Super ClassLipids and lipid-like molecules  
ClassPrenol lipids  
Sub ClassMonoterpenoids  
Direct ParentIridoids and derivatives  
Alternative Parents
Substituents
  • Monocyclic monoterpenoid
    • 

  • 11-noriridane monoterpenoid
    • 

  • Secondary alcohol
    • 

  • Monocarboxylic acid or derivatives
    • 

  • Carboxylic acid
    • 

  • Carboxylic acid derivative
    • 

  • Organic oxygen compound
    • 

  • Organic oxide
    • 

  • Hydrocarbon derivative
    • 

  • Primary alcohol
    • 

  • Organooxygen compound
    • 

  • Carbonyl group
    • 

  • Alcohol
    • 

  • Aliphatic homomonocyclic compound
Molecular FrameworkAliphatic homomonocyclic 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
logP-1.8ChemAxon
pKa (Strongest Acidic)4.3ChemAxon
pKa (Strongest Basic)-2.4ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area97.99 ŲChemAxon
Rotatable Bond Count4ChemAxon
Refractivity48.85 m³·mol⁻¹ChemAxon
Polarizability19.89 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDNot Available
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID8925937  
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound10750613  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. LOTUS database [Link]