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Showing NP-Card for Genipin (NP0050278)

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Record Information
Version2.0
Created at2022-04-27 20:51:05 UTC
Updated at2022-04-27 20:51:05 UTC
NP-MRD IDNP0050278
Secondary Accession NumbersNone
Natural Product Identification
Common NameGenipin
DescriptionGenipin 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. Genipin is found in Apodytes dimidiata, Eucommia ulmoides, Gardenia jasminoides , Garrya elliptica, Genipa americana and Rothmannia globosa. Genipin was first documented in 2022 (PMID: 35466258). Based on a literature review a small amount of articles have been published on Genipin (PMID: 35453566) (PMID: 35450637) (PMID: 35409033) (PMID: 35404375).
Structure
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MOLSDFPDBSMILESInChI

MOL for NP0050278 (Genipin)


  Mrv1652304272222512D          

 16 17  0  0  1  0            999 V2000
    0.6411   -1.1104    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.6411   -0.2854    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.3556    0.1271    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.0701   -0.2854    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0701   -1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3556   -1.5229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3556   -2.3479    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6411   -2.7604    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0701   -2.7604    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0701   -3.5854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3556    0.9521    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1435   -0.0305    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6284   -0.6979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1435   -1.3654    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3984    0.7541    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2054    0.9256    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  1  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  7  9  1  0  0  0  0
  9 10  1  0  0  0  0
  3 11  1  6  0  0  0
  2 12  1  1  0  0  0
 12 13  2  0  0  0  0
 13 14  1  0  0  0  0
  1 14  1  1  0  0  0
 12 15  1  0  0  0  0
 15 16  1  0  0  0  0
M  END
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3D MOL for NP0050278 (Genipin)

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3D SDF for NP0050278 (Genipin)

  Mrv1652304272222512D          

 16 17  0  0  1  0            999 V2000
    0.6411   -1.1104    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.6411   -0.2854    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.3556    0.1271    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.0701   -0.2854    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0701   -1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3556   -1.5229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3556   -2.3479    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6411   -2.7604    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0701   -2.7604    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0701   -3.5854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3556    0.9521    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1435   -0.0305    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6284   -0.6979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1435   -1.3654    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3984    0.7541    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2054    0.9256    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  1  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  7  9  1  0  0  0  0
  9 10  1  0  0  0  0
  3 11  1  6  0  0  0
  2 12  1  1  0  0  0
 12 13  2  0  0  0  0
 13 14  1  0  0  0  0
  1 14  1  1  0  0  0
 12 15  1  0  0  0  0
 15 16  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0050278

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC(=O)C1=CO[C@@H](O)[C@H]2[C@@H]1CC=C2CO

> <INCHI_IDENTIFIER>
InChI=1S/C11H14O5/c1-15-10(13)8-5-16-11(14)9-6(4-12)2-3-7(8)9/h2,5,7,9,11-12,14H,3-4H2,1H3/t7-,9-,11-/m1/s1

> <INCHI_KEY>
AZKVWQKMDGGDSV-BCMRRPTOSA-N

> <FORMULA>
C11H14O5

> <MOLECULAR_WEIGHT>
226.228

> <EXACT_MASS>
226.084123551

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
30

> <JCHEM_AVERAGE_POLARIZABILITY>
22.200163087813827

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
methyl (1R,4aS,7aS)-1-hydroxy-7-(hydroxymethyl)-1H,4aH,5H,7aH-cyclopenta[c]pyran-4-carboxylate

> <ALOGPS_LOGP>
0.07

> <JCHEM_LOGP>
-0.443895659666666

> <ALOGPS_LOGS>
-1.50

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
15.150537367169974

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.036945977145045

> <JCHEM_PKA_STRONGEST_BASIC>
-2.7354177854672015

> <JCHEM_POLAR_SURFACE_AREA>
75.99000000000001

> <JCHEM_REFRACTIVITY>
56.093300000000006

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
7.18e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
genipin

> <JCHEM_VEBER_RULE>
0

$$$$

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3D-SDF for NP0050278 (Genipin)
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PDB for NP0050278 (Genipin)
HEADER    PROTEIN                                 27-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   27-APR-22         0                                  
HETATM    1  C   UNK     0       1.197  -2.073   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.197  -0.533   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.530   0.237   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       3.864  -0.533   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       3.864  -2.073   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.530  -2.843   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       2.530  -4.383   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       1.197  -5.153   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0       3.864  -5.153   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0       3.864  -6.693   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0       2.530   1.777   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0      -0.268  -0.057   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -1.173  -1.303   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -0.268  -2.549   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -0.744   1.408   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0      -2.250   1.728   0.000  0.00  0.00           O+0
CONECT    1    2    6   14                                                  
CONECT    2    1    3   12                                                  
CONECT    3    2    4   11                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    1    7                                                  
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10                                                       
CONECT   10    9                                                            
CONECT   11    3                                                            
CONECT   12    2   13   15                                                  
CONECT   13   12   14                                                       
CONECT   14   13    1                                                       
CONECT   15   12   16                                                       
CONECT   16   15                                                            
MASTER        0    0    0    0    0    0    0    0   16    0   34    0
END

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3D PDB for NP0050278 (Genipin)
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SMILES for NP0050278 (Genipin)
COC(=O)C1=CO[C@@H](O)[C@H]2[C@@H]1CC=C2CO
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INCHI for NP0050278 (Genipin)
InChI=1S/C11H14O5/c1-15-10(13)8-5-16-11(14)9-6(4-12)2-3-7(8)9/h2,5,7,9,11-12,14H,3-4H2,1H3/t7-,9-,11-/m1/s1
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SynonymsNot Available
Chemical FormulaC11H14O5
Average Mass226.2280 Da
Monoisotopic Mass226.08412 Da
IUPAC Namemethyl (1R,4aS,7aS)-1-hydroxy-7-(hydroxymethyl)-1H,4aH,5H,7aH-cyclopenta[c]pyran-4-carboxylate
Traditional Namegenipin
CAS Registry NumberNot Available
SMILES
COC(=O)C1=CO[C@@H](O)[C@H]2[C@@H]1CC=C2CO
InChI Identifier
InChI=1S/C11H14O5/c1-15-10(13)8-5-16-11(14)9-6(4-12)2-3-7(8)9/h2,5,7,9,11-12,14H,3-4H2,1H3/t7-,9-,11-/m1/s1
InChI KeyAZKVWQKMDGGDSV-BCMRRPTOSA-N
Experimental Spectra
Not Available
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Apodytes dimidiataLOTUS Database
Eucommia ulmoidesLOTUS Database
Gardenia jasminoidesPlant
Garrya ellipticaLOTUS Database
Genipa americanaPlant
Rothmannia globosaPlant
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
  • Iridoid-skeleton
    • 

  • Bicyclic monoterpenoid
    • 

  • Methyl ester
    • 

  • Vinylogous ester
    • 

  • Alpha,beta-unsaturated carboxylic ester
    • 

  • Enoate ester
    • 

  • Carboxylic acid ester
    • 

  • Hemiacetal
    • 

  • Carboxylic acid derivative
    • 

  • Oxacycle
    • 

  • Monocarboxylic acid or derivatives
    • 

  • Organoheterocyclic compound
    • 

  • Hydrocarbon derivative
    • 

  • Organic oxide
    • 

  • Alcohol
    • 

  • Organic oxygen compound
    • 

  • Organooxygen compound
    • 

  • Primary alcohol
    • 

  • Carbonyl group
    • 

  • Aliphatic heteropolycyclic compound
Molecular FrameworkAliphatic heteropolycyclic compounds
External Descriptors
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
logP0.07ALOGPS
logP-0.44ChemAxon
logS-1.5ALOGPS
pKa (Strongest Acidic)12.04ChemAxon
pKa (Strongest Basic)-2.7ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area75.99 ŲChemAxon
Rotatable Bond Count3ChemAxon
Refractivity56.09 m³·mol⁻¹ChemAxon
Polarizability22.2 ųChemAxon
Number of Rings2ChemAxon
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 IDC00000321  
Chemspider ID390864  
KEGG Compound IDC09780  
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkGenipin  
METLIN IDNot Available
PubChem Compound442424  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDrw1851921  
References
General References
  1. Min Q, Tian D, Zhang Y, Wang C, Wan Y, Wu J: Strong and Elastic Chitosan/Silk Fibroin Hydrogels Incorporated with Growth-Factor-Loaded Microspheres for Cartilage Tissue Engineering. Biomimetics (Basel). 2022 Apr 7;7(2). pii: biomimetics7020041. doi: 10.3390/biomimetics7020041. [PubMed:35466258  ] 
  2. Salleh A, Mustafa N, Teow YH, Fatimah MN, Khairudin FA, Ahmad I, Fauzi MB: Dual-Layered Approach of Ovine Collagen-Gelatin/Cellulose Hybrid Biomatrix Containing Graphene Oxide-Silver Nanoparticles for Cutaneous Wound Healing: Fabrication, Physicochemical, Cytotoxicity and Antibacterial Characterisation. Biomedicines. 2022 Mar 31;10(4). pii: biomedicines10040816. doi: 10.3390/biomedicines10040816. [PubMed:35453566  ] 
  3. Gruppuso M, Iorio F, Turco G, Marsich E, Porrelli D: Hyaluronic acid/lactose-modified chitosan electrospun wound dressings - Crosslinking and stability criticalities. Carbohydr Polym. 2022 Jul 15;288:119375. doi: 10.1016/j.carbpol.2022.119375. Epub 2022 Mar 18. [PubMed:35450637  ] 
  4. Feng C, Anger EE, Zhang X, Su S, Su C, Zhao S, Yu F, Li J: Protective Effects of Mitochondrial Uncoupling Protein 2 against Aristolochic Acid I-Induced Toxicity in HK-2 Cells. Int J Mol Sci. 2022 Mar 27;23(7). pii: ijms23073674. doi: 10.3390/ijms23073674. [PubMed:35409033  ] 
  5. Lau K, Reichheld S, Sharpe S, Cerruti M: Globule and fiber formation with elastin-like polypeptides: a balance of coacervation and crosslinking. Soft Matter. 2022 Apr 20;18(16):3257-3266. doi: 10.1039/d2sm00049k. [PubMed:35404375  ]