Showing NP-Card for Isopentenyl pyrophosphate (NP0044474)

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Record Information
Version2.0
Created at2022-02-14 20:57:24 UTC
Updated at2022-03-10 22:21:28 UTC
NP-MRD IDNP0044474
Secondary Accession NumbersNone
Natural Product Identification
Common NameIsopentenyl pyrophosphate
DescriptionIsopentenyl pyrophosphate, also known as IPP or delta(3)-isopentenyl-PP, belongs to the class of organic compounds known as isoprenoid phosphates. These are prenol lipids containing a phosphate group linked to an isoprene (2-methylbuta-1,3-diene) unit. Isopentenyl pyrophosphate is a very hydrophobic molecule, practically insoluble (in water), and relatively neutral. Isopentenyl pyrophosphate is expected to be in Cannabis as all living plants are known to produce and metabolize it.
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0044474 (Isopentenyl pyrophosphate)

  Mrv1652309042000212D          

 14 13  0  0  0  0            999 V2000
   16.3566   -5.2503    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   14.9279   -5.2503    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.6422   -4.0128    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   14.2134   -4.8377    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.0711   -4.0127    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.7856   -5.2503    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.4990   -5.2503    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.7845   -4.8377    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.0699   -5.2503    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.7844   -4.0131    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.0711   -4.8377    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   17.0712   -5.6627    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.6422   -4.8377    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   15.6422   -5.6629    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 13  3  2  0  0  0  0
 11  5  2  0  0  0  0
  8 10  2  0  0  0  0
 11 12  1  0  0  0  0
 13 14  1  0  0  0  0
 11  6  1  0  0  0  0
  1 11  1  0  0  0  0
  2  4  1  0  0  0  0
  4  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
 13  2  1  0  0  0  0
 13  1  1  0  0  0  0
M  END
Download

3D MOL for NP0044474 (Isopentenyl pyrophosphate)

     RDKit          3D

 26 25  0  0  0  0  0  0  0  0999 V2000
   -3.8791    0.3156   -1.2168 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0634   -0.0086   -0.2254 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1848   -1.3751    0.3480 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0832    0.9653    0.2713 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6498    0.4922    0.1430 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1570    1.5082    0.6484 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7857    1.1485    0.5827 P   0  0  1  0  0  5  0  0  0  0  0  0
    2.5335    2.4209    0.2473 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3922    0.5859    2.0518 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0213    0.0288   -0.6686 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5481   -0.6872   -0.5671 P   0  0  1  0  0  5  0  0  0  0  0  0
    3.5351   -1.9010   -1.4616 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.7181    0.4452   -1.0671 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.8058   -1.0977    1.0526 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8600    1.3004   -1.6993 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6103   -0.3794   -1.6033 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1929   -1.7898    0.6363 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9042   -1.4083    1.2003 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5862   -2.0645   -0.4238 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2400    1.2304    1.3364 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1539    1.9118   -0.3025 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4674   -0.4181    0.7616 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3538    0.3360   -0.9111 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7268    0.0334    2.5296 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5708    0.2515   -0.5770 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4345   -1.8441    1.1501 H   0  0  0  0  0  0  0  0  0  0  0  0
  3  2  1  0
  2  1  2  3
  2  4  1  0
  4  5  1  0
  5  6  1  0
  7  6  1  1
  7  9  1  0
  7  8  2  0
  7 10  1  0
 11 10  1  1
 11 13  1  0
 11 14  1  0
 11 12  2  0
  3 17  1  0
  3 18  1  0
  3 19  1  0
  1 15  1  0
  1 16  1  0
  4 20  1  0
  4 21  1  0
  5 22  1  0
  5 23  1  0
  9 24  1  0
 13 25  1  0
 14 26  1  0
M  END
Download

3D SDF for NP0044474 (Isopentenyl pyrophosphate)

  Mrv1652309042000212D          

 14 13  0  0  0  0            999 V2000
   16.3566   -5.2503    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   14.9279   -5.2503    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.6422   -4.0128    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   14.2134   -4.8377    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.0711   -4.0127    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.7856   -5.2503    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.4990   -5.2503    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.7845   -4.8377    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.0699   -5.2503    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.7844   -4.0131    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.0711   -4.8377    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   17.0712   -5.6627    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.6422   -4.8377    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   15.6422   -5.6629    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 13  3  2  0  0  0  0
 11  5  2  0  0  0  0
  8 10  2  0  0  0  0
 11 12  1  0  0  0  0
 13 14  1  0  0  0  0
 11  6  1  0  0  0  0
  1 11  1  0  0  0  0
  2  4  1  0  0  0  0
  4  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
 13  2  1  0  0  0  0
 13  1  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0044474

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(=C)CCOP(O)(=O)OP(O)(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C5H12O7P2/c1-5(2)3-4-11-14(9,10)12-13(6,7)8/h1,3-4H2,2H3,(H,9,10)(H2,6,7,8)

> <INCHI_KEY>
NUHSROFQTUXZQQ-UHFFFAOYSA-N

> <FORMULA>
C5H12O7P2

> <MOLECULAR_WEIGHT>
246.0921

> <EXACT_MASS>
246.005825762

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
26

> <JCHEM_AVERAGE_POLARIZABILITY>
19.011958475186823

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
({hydroxy[(3-methylbut-3-en-1-yl)oxy]phosphoryl}oxy)phosphonic acid

> <ALOGPS_LOGP>
0.04

> <JCHEM_LOGP>
0.19933072100000007

> <ALOGPS_LOGS>
-1.57

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
3.219951501702814

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.7784542453586973

> <JCHEM_POLAR_SURFACE_AREA>
113.29

> <JCHEM_REFRACTIVITY>
48.2068

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.69e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
isopentenyl-diphosphate

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0044474 (Isopentenyl pyrophosphate)

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PDB for NP0044474 (Isopentenyl pyrophosphate)
HEADER    PROTEIN                                 04-SEP-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-SEP-20         0                                  
HETATM    1  O   UNK     0      30.532  -9.801   0.000  0.00  0.00           O+0
HETATM    2  O   UNK     0      27.865  -9.801   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0      29.199  -7.491   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0      26.532  -9.030   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0      31.866  -7.490   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0      33.200  -9.801   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0      25.198  -9.801   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      23.864  -9.030   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      22.530  -9.801   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      23.864  -7.491   0.000  0.00  0.00           C+0
HETATM   11  P   UNK     0      31.866  -9.030   0.000  0.00  0.00           P+0
HETATM   12  O   UNK     0      31.866 -10.570   0.000  0.00  0.00           O+0
HETATM   13  P   UNK     0      29.199  -9.030   0.000  0.00  0.00           P+0
HETATM   14  O   UNK     0      29.199 -10.571   0.000  0.00  0.00           O+0
CONECT    1   11   13                                                       
CONECT    2    4   13                                                       
CONECT    3   13                                                            
CONECT    4    2    7                                                       
CONECT    5   11                                                            
CONECT    6   11                                                            
CONECT    7    4    8                                                       
CONECT    8   10    7    9                                                  
CONECT    9    8                                                            
CONECT   10    8                                                            
CONECT   11    5   12    6    1                                             
CONECT   12   11                                                            
CONECT   13    3   14    2    1                                             
CONECT   14   13                                                            
MASTER        0    0    0    0    0    0    0    0   14    0   26    0
END

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3D PDB for NP0044474 (Isopentenyl pyrophosphate)
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SMILES for NP0044474 (Isopentenyl pyrophosphate)
CC(=C)CCOP(O)(=O)OP(O)(O)=O
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INCHI for NP0044474 (Isopentenyl pyrophosphate)
InChI=1S/C5H12O7P2/c1-5(2)3-4-11-14(9,10)12-13(6,7)8/h1,3-4H2,2H3,(H,9,10)(H2,6,7,8)
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View in JSmol
Synonyms
Chemical FormulaC5H12O7P2
Average Mass246.0921 Da
Monoisotopic Mass246.00583 Da
IUPAC Name({hydroxy[(3-methylbut-3-en-1-yl)oxy]phosphoryl}oxy)phosphonic acid
Traditional Nameisopentenyl-diphosphate
CAS Registry Number358-71-4
SMILES
CC(=C)CCOP(O)(=O)OP(O)(O)=O
InChI Identifier
InChI=1S/C5H12O7P2/c1-5(2)3-4-11-14(9,10)12-13(6,7)8/h1,3-4H2,2H3,(H,9,10)(H2,6,7,8)
InChI KeyNUHSROFQTUXZQQ-UHFFFAOYSA-N
Experimental Spectra
Not Available
Predicted Spectra
Chemical Shift Submissions
Not Available
Species
Species of Origin
Chemical Taxonomy
Description Belongs to the class of organic compounds known as isoprenoid phosphates. These are prenol lipids containing a phosphate group linked to an isoprene (2-methylbuta-1,3-diene) unit.
KingdomOrganic compounds  
Super ClassLipids and lipid-like molecules  
ClassPrenol lipids  
Sub ClassIsoprenoid phosphates  
Direct ParentIsoprenoid phosphates  
Alternative Parents
Substituents
  • Organic pyrophosphate
    • 

  • Isoprenoid phosphate
    • 

  • Monoalkyl phosphate
    • 

  • Alkyl phosphate
    • 

  • Phosphoric acid ester
    • 

  • Organic phosphoric acid derivative
    • 

  • Organic oxygen compound
    • 

  • Organic oxide
    • 

  • Hydrocarbon derivative
    • 

  • Organooxygen compound
    • 

  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic 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
logP0.04ALOGPS
logP0.2ChemAxon
logS-1.6ALOGPS
pKa (Strongest Acidic)1.78ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area113.29 ŲChemAxon
Rotatable Bond Count6ChemAxon
Refractivity48.21 m³·mol⁻¹ChemAxon
Polarizability19.01 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0001347  
DrugBank IDDB04714  
Phenol Explorer Compound IDNot Available
FoodDB IDFDB030946  
KNApSAcK IDC00000848  
Chemspider ID1158  
KEGG Compound IDC00129  
BioCyc IDDELTA3-ISOPENTENYL-PP  
BiGG ID33956  
Wikipedia LinkIsopentenyl pyrophosphate  
METLIN ID6181  
PubChem Compound1195  
PDB IDNot Available
ChEBI ID16584  
Good Scents IDNot Available
References
General References
  1. Daubenberger CA, Salomon M, Vecino W, Hubner B, Troll H, Rodriques R, Patarroyo ME, Pluschke G: Functional and structural similarity of V gamma 9V delta 2 T cells in humans and Aotus monkeys, a primate infection model for Plasmodium falciparum malaria. J Immunol. 2001 Dec 1;167(11):6421-30. doi: 10.4049/jimmunol.167.11.6421. [PubMed:11714808  ] 
  2. Lafont V, Liautard J, Sable-Teychene M, Sainte-Marie Y, Favero J: Isopentenyl pyrophosphate, a mycobacterial non-peptidic antigen, triggers delayed and highly sustained signaling in human gamma delta T lymphocytes without inducing eown-modulation of T cell antigen receptor. J Biol Chem. 2001 May 11;276(19):15961-7. doi: 10.1074/jbc.M008684200. Epub 2001  Feb 13. [PubMed:11278429  ] 
  3. Ling S, Wu Y, Zheng J, Linden J, Holoshitz J: Genoprotective pathways. II. Attenuation of oxidative DNA damage by isopentenyl diphosphate. Mutat Res. 2004 Oct 4;554(1-2):33-43. doi: 10.1016/j.mrfmmm.2004.02.015. [PubMed:15450402  ] 
  4. Tong H, Kuder CH, Wasko BM, Hohl RJ: Quantitative determination of isopentenyl diphosphate in cultured mammalian cells. Anal Biochem. 2013 Feb 1;433(1):36-42. doi: 10.1016/j.ab.2012.09.001. Epub 2012 Sep 19. [PubMed:23000003  ]