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Showing NP-Card for IM-2 (NP0050297)

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Record Information
Version2.0
Created at2022-04-27 20:51:47 UTC
Updated at2022-04-27 20:51:48 UTC
NP-MRD IDNP0050297
Secondary Accession NumbersNone
Natural Product Identification
Common NameIM-2
DescriptionIM-2 belongs to the class of organic compounds known as gamma butyrolactones. Gamma butyrolactones are compounds containing a gamma butyrolactone moiety, which consists of an aliphatic five-member ring with four carbon atoms, one oxygen atom, and bears a ketone group on the carbon adjacent to the oxygen atom. IM-2 is found in Streptomyces lavendulae and Streptomyces sp. strain FRI-5. Based on a literature review very few articles have been published on IM-2.
Structure
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MOLSDFPDBSMILESInChI

MOL for NP0050297 (IM-2)


  Mrv1652304272222512D          

 13 13  0  0  1  0            999 V2000
    0.9803   -0.1553    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1553   -0.1553    0.0000 C   0  0  0  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
    0.5678    1.1143    0.0000 C   0  0  1  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
    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
   -0.8843    0.8843    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.4974    0.3323    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2820    0.5872    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8951    0.0352    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0558    1.6913    0.0000 O   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  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  1  6  1  0  0  0  0
  5  7  1  6  0  0  0
  7  8  1  0  0  0  0
  4  9  1  1  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
  9 13  1  1  0  0  0
M  END
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3D MOL for NP0050297 (IM-2)

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3D SDF for NP0050297 (IM-2)

  Mrv1652304272222512D          

 13 13  0  0  1  0            999 V2000
    0.9803   -0.1553    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1553   -0.1553    0.0000 C   0  0  0  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
    0.5678    1.1143    0.0000 C   0  0  1  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
    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
   -0.8843    0.8843    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.4974    0.3323    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2820    0.5872    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8951    0.0352    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0558    1.6913    0.0000 O   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  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  1  6  1  0  0  0  0
  5  7  1  6  0  0  0
  7  8  1  0  0  0  0
  4  9  1  1  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
  9 13  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0050297

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CCC[C@@H](O)[C@H]1[C@H](CO)COC1=O

> <INCHI_IDENTIFIER>
InChI=1S/C9H16O4/c1-2-3-7(11)8-6(4-10)5-13-9(8)12/h6-8,10-11H,2-5H2,1H3/t6-,7-,8-/m1/s1

> <INCHI_KEY>
QXCJMSMGYHDDLQ-BWZBUEFSSA-N

> <FORMULA>
C9H16O4

> <MOLECULAR_WEIGHT>
188.223

> <EXACT_MASS>
188.104858995

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
29

> <JCHEM_AVERAGE_POLARIZABILITY>
19.668170490269333

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(3R,4R)-3-[(1R)-1-hydroxybutyl]-4-(hydroxymethyl)oxolan-2-one

> <ALOGPS_LOGP>
0.08

> <JCHEM_LOGP>
-0.234716551333333

> <ALOGPS_LOGS>
0.09

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
15.451277550083422

> <JCHEM_PKA_STRONGEST_ACIDIC>
14.597530979693182

> <JCHEM_PKA_STRONGEST_BASIC>
-2.639868419810756

> <JCHEM_POLAR_SURFACE_AREA>
66.76

> <JCHEM_REFRACTIVITY>
46.502599999999994

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.34e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(3R,4R)-3-[(1R)-1-hydroxybutyl]-4-(hydroxymethyl)oxolan-2-one

> <JCHEM_VEBER_RULE>
0

$$$$

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3D-SDF for NP0050297 (IM-2)
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PDB for NP0050297 (IM-2)
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  O   UNK     0       1.830  -0.290   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       0.290  -0.290   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0      -0.615  -1.536   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0      -0.186   1.175   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.060   2.080   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.306   1.175   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       1.060   3.620   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       2.393   4.390   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0      -1.651   1.651   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -2.795   0.620   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -4.260   1.096   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -5.404   0.066   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0      -1.971   3.157   0.000  0.00  0.00           O+0
CONECT    1    2    6                                                       
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5    9                                                  
CONECT    5    4    6    7                                                  
CONECT    6    5    1                                                       
CONECT    7    5    8                                                       
CONECT    8    7                                                            
CONECT    9    4   10   13                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11                                                            
CONECT   13    9                                                            
MASTER        0    0    0    0    0    0    0    0   13    0   26    0
END

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3D PDB for NP0050297 (IM-2)
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SMILES for NP0050297 (IM-2)
CCC[C@@H](O)[C@H]1[C@H](CO)COC1=O
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INCHI for NP0050297 (IM-2)
InChI=1S/C9H16O4/c1-2-3-7(11)8-6(4-10)5-13-9(8)12/h6-8,10-11H,2-5H2,1H3/t6-,7-,8-/m1/s1
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SynonymsNot Available
Chemical FormulaC9H16O4
Average Mass188.2230 Da
Monoisotopic Mass188.10486 Da
IUPAC Name(3R,4R)-3-[(1R)-1-hydroxybutyl]-4-(hydroxymethyl)oxolan-2-one
Traditional Name(3R,4R)-3-[(1R)-1-hydroxybutyl]-4-(hydroxymethyl)oxolan-2-one
CAS Registry NumberNot Available
SMILES
CCC[C@@H](O)[C@H]1[C@H](CO)COC1=O
InChI Identifier
InChI=1S/C9H16O4/c1-2-3-7(11)8-6(4-10)5-13-9(8)12/h6-8,10-11H,2-5H2,1H3/t6-,7-,8-/m1/s1
InChI KeyQXCJMSMGYHDDLQ-BWZBUEFSSA-N
Experimental Spectra
Not Available
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Streptomyces lavendulaeLOTUS Database
Streptomyces sp. strain FRI-5Bacteria
Chemical Taxonomy
Description Belongs to the class of organic compounds known as gamma butyrolactones. Gamma butyrolactones are compounds containing a gamma butyrolactone moiety, which consists of an aliphatic five-member ring with four carbon atoms, one oxygen atom, and bears a ketone group on the carbon adjacent to the oxygen atom.
KingdomOrganic compounds  
Super ClassOrganoheterocyclic compounds  
ClassLactones  
Sub ClassGamma butyrolactones  
Direct ParentGamma butyrolactones  
Alternative Parents
Substituents
  • Gamma butyrolactone
    • 

  • Oxolane
    • 

  • Secondary alcohol
    • 

  • Carboxylic acid ester
    • 

  • Oxacycle
    • 

  • Monocarboxylic acid or derivatives
    • 

  • Carboxylic acid derivative
    • 

  • Organic oxygen compound
    • 

  • Organic oxide
    • 

  • Hydrocarbon derivative
    • 

  • Primary alcohol
    • 

  • Organooxygen compound
    • 

  • Carbonyl group
    • 

  • Alcohol
    • 

  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic 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
logP0.08ALOGPS
logP-0.23ChemAxon
logS0.09ALOGPS
pKa (Strongest Acidic)14.6ChemAxon
pKa (Strongest Basic)-2.6ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area66.76 ŲChemAxon
Rotatable Bond Count4ChemAxon
Refractivity46.5 m³·mol⁻¹ChemAxon
Polarizability19.67 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDNot Available
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDC00000368  
Chemspider ID10004820  
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNova-C  
METLIN IDNot Available
PubChem Compound11830173  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References