MiMeDB: Showing metabocard for (+)-copalyl diphosphate (MMDBc0054018)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2022-06-05 22:46:02 UTC

Update Date

2022-09-01 02:26:41 UTC

Metabolite ID

MMDBc0054018

Metabolite Identification

Common Name

(+)-copalyl diphosphate

Description

Copalyl diphosphate belongs to the class of organic compounds known as diterpenoids. These are terpene compounds formed by four isoprene units. Copalyl diphosphate is a very hydrophobic molecule, practically insoluble (in water), and relatively neutral.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652301072004032D          

 29 30  0  0  1  0            999 V2000
    1.4289   -4.1250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -1.6500    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.8579    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3276    0.6320    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3882    0.6320    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -1.2375    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.1434   -2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -4.1250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -5.3625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -6.1875    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1105   -6.1875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5395   -6.1875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -7.0125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -7.4250    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -7.8375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0164   -8.1395    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8414   -6.7105    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
  5  4  1  1  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  6  8  1  0  0  0  0
  8  9  1  0  0  0  0
 10  9  1  1  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 11 13  1  0  0  0  0
 11 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
  5 17  1  0  0  0  0
 10 17  1  0  0  0  0
 17 18  1  1  0  0  0
  2 19  2  0  0  0  0
 19 20  1  0  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
 22 23  1  0  0  0  0
 22 24  2  0  0  0  0
 22 25  1  0  0  0  0
 25 26  1  0  0  0  0
 26 27  1  0  0  0  0
 26 28  1  0  0  0  0
 26 29  2  0  0  0  0
M  END


  Mrv1652301072004032D          

 29 30  0  0  1  0            999 V2000
    1.4289   -4.1250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -1.6500    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.8579    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3276    0.6320    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3882    0.6320    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -1.2375    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.1434   -2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -4.1250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -5.3625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -6.1875    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1105   -6.1875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5395   -6.1875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -7.0125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -7.4250    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -7.8375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0164   -8.1395    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8414   -6.7105    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
  5  4  1  1  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  6  8  1  0  0  0  0
  8  9  1  0  0  0  0
 10  9  1  1  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 11 13  1  0  0  0  0
 11 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
  5 17  1  0  0  0  0
 10 17  1  0  0  0  0
 17 18  1  1  0  0  0
  2 19  2  0  0  0  0
 19 20  1  0  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
 22 23  1  0  0  0  0
 22 24  2  0  0  0  0
 22 25  1  0  0  0  0
 25 26  1  0  0  0  0
 26 27  1  0  0  0  0
 26 28  1  0  0  0  0
 26 29  2  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0054018

> <DATABASE_NAME>
MIME

> <SMILES>
C\C(CC[C@H]1C(=C)CC[C@H]2C(C)(C)CCC[C@]12C)=C/COP(O)(=O)OP(O)(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C20H36O7P2/c1-15(11-14-26-29(24,25)27-28(21,22)23)7-9-17-16(2)8-10-18-19(3,4)12-6-13-20(17,18)5/h11,17-18H,2,6-10,12-14H2,1,3-5H3,(H,24,25)(H2,21,22,23)/b15-11+/t17-,18-,20+/m0/s1

> <INCHI_KEY>
JCAIWDXKLCEQEO-ATPOGHATSA-N

> <FORMULA>
C20H36O7P2

> <MOLECULAR_WEIGHT>
450.449

> <EXACT_MASS>
450.193627495

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
65

> <JCHEM_AVERAGE_POLARIZABILITY>
46.322058150866816

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
[({[(2E)-5-[(1S,4aS,8aS)-5,5,8a-trimethyl-2-methylidene-decahydronaphthalen-1-yl]-3-methylpent-2-en-1-yl]oxy}(hydroxy)phosphoryl)oxy]phosphonic acid

> <JCHEM_LOGP>
4.613945935999999

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
3.204340614405425

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.7672186921378312

> <JCHEM_POLAR_SURFACE_AREA>
113.29000000000002

> <JCHEM_REFRACTIVITY>
113.79959999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
copalyl diphosphate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 07-JAN-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   07-JAN-20         0                                  
HETATM    1  C   UNK     0       2.667  -7.700   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.334  -6.930   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.334  -5.390   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.667  -4.620   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.000  -3.080   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       5.335   0.000   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       4.345   1.180   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       6.325   1.180   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       6.668  -0.770   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       6.668  -2.310   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       5.335  -3.080   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       4.001  -3.850   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       0.000  -7.700   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       0.000  -9.240   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0       1.334 -10.010   0.000  0.00  0.00           O+0
HETATM   22  P   UNK     0       1.334 -11.550   0.000  0.00  0.00           P+0
HETATM   23  O   UNK     0      -0.206 -11.550   0.000  0.00  0.00           O+0
HETATM   24  O   UNK     0       2.874 -11.550   0.000  0.00  0.00           O+0
HETATM   25  O   UNK     0       1.334 -13.090   0.000  0.00  0.00           O+0
HETATM   26  P   UNK     0       2.667 -13.860   0.000  0.00  0.00           P+0
HETATM   27  O   UNK     0       4.001 -14.630   0.000  0.00  0.00           O+0
HETATM   28  O   UNK     0       1.897 -15.194   0.000  0.00  0.00           O+0
HETATM   29  O   UNK     0       3.437 -12.526   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   19                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6   17                                                  
CONECT    6    5    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11   17                                                  
CONECT   11   10   12   13   14                                             
CONECT   12   11                                                            
CONECT   13   11                                                            
CONECT   14   11   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16    5   10   18                                             
CONECT   18   17                                                            
CONECT   19    2   20                                                       
CONECT   20   19   21                                                       
CONECT   21   20   22                                                       
CONECT   22   21   23   24   25                                             
CONECT   23   22                                                            
CONECT   24   22                                                            
CONECT   25   22   26                                                       
CONECT   26   25   27   28   29                                             
CONECT   27   26                                                            
CONECT   28   26                                                            
CONECT   29   26                                                            
MASTER        0    0    0    0    0    0    0    0   29    0   60    0
END

Synonyms

Value	Source
(+)-Copalyl diphosphate	Kegg
Labdadienyl diphosphate	Kegg
(+)-Copalyl diphosphoric acid	Generator
Labdadienyl diphosphoric acid	Generator
Copalyl diphosphoric acid	Generator

Molecular Formula

C₂₀H₃₆O₇P₂

Average Mass

450.449

Monoisotopic Mass

450.193627495

IUPAC Name

[({[(2E)-5-[(1S,4aS,8aS)-5,5,8a-trimethyl-2-methylidene-decahydronaphthalen-1-yl]-3-methylpent-2-en-1-yl]oxy}(hydroxy)phosphoryl)oxy]phosphonic acid

Traditional Name

copalyl diphosphate

CAS Registry Number

Not Available

SMILES

C\C(CC[C@H]1C(=C)CC[C@H]2C(C)(C)CCC[C@]12C)=C/COP(O)(=O)OP(O)(O)=O

InChI Identifier

InChI=1S/C20H36O7P2/c1-15(11-14-26-29(24,25)27-28(21,22)23)7-9-17-16(2)8-10-18-19(3,4)12-6-13-20(17,18)5/h11,17-18H,2,6-10,12-14H2,1,3-5H3,(H,24,25)(H2,21,22,23)/b15-11+/t17-,18-,20+/m0/s1

InChI Key

JCAIWDXKLCEQEO-ATPOGHATSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as diterpenoids. These are terpene compounds formed by four isoprene units.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Diterpenoids

Direct Parent

Diterpenoids

Alternative Parents

Substituents

Diterpenoid
Labdane diterpenoid
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 homopolycyclic compound

Molecular Framework

Aliphatic homopolycyclic compounds

External Descriptors

copalyl diphosphate (CHEBI:30939 )
Labdane and halimane diterpenoids (C11901 )
Labdanes (C11901 )
Labdane and halimane diterpenoids (LMPR0104030002 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
logP	4.61	ChemAxon
pKa (Strongest Acidic)	1.77	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	113.29 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	113.8 m³·mol⁻¹	ChemAxon
Polarizability	46.32 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Spectrum Type	Description	Splash Key	Deposition Date	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_1) - 70eV, Positive	Not Available	2022-08-08	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	Not Available	2022-08-09	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	Not Available	2022-08-09	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	Not Available	2022-08-09	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	Not Available	2022-08-09	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	Not Available	2022-08-09	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	Not Available	2022-08-09	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Protein ID	Protein Name	Protein Type	Uniprot ID	Species

Human Pathways

Pathways

Name	SMPDB/PathBank

Metabolic Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference
MMDBr0014439	(2E,6E,10E)-geranylgeranyl diphosphate	(+)-copalyl diphosphate	Copalyl diphosphate synthase	Synthesis	RHEA	34755880
MMDBr0014440	(2E,6E,10E)-geranylgeranyl diphosphate	(+)-copalyl diphosphate	Copalyl diphosphate synthase	Synthesis	RHEA	34755880
MMDBr0014643	(+)-copalyl diphosphate	diphosphate	Phyllocladan-16-alpha-ol synthase	Synthesis	RHEA	34755880
MMDBr0015708	(+)-copalyl diphosphate	(+)-copalol	Tuberculosinyl adenosine transferase	Transfer of adenosine	RHEA	34755880
MMDBr0015709	(+)-copalyl diphosphate	diphosphate	Tuberculosinyl adenosine transferase	Transfer of adenosine	RHEA	34755880
MMDBr0015710	(+)-copalyl diphosphate	13-epi-manool	Tuberculosinyl adenosine transferase	Transfer of adenosine	RHEA	34755880
MMDBr0016750	(+)-copalyl diphosphate	(12E)-labda-8(17),12,14-triene	(12E)-labda-8(17),12,14-triene synthase	Synthesis	RHEA	34755880

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Evidence Type	Host and Biospecimen	Data Source	Reference

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
Bacteria	Actinobacteria	3	Human
Eukaryota/Fungi	Ascomycota	5	Human feces

Exposure Sources

Source Type	Source Sub-type	Species	Data Source	Reference

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

C00000876

Chemspider ID

4445249

KEGG Compound ID

C11901

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

5281990

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Bansal P, Morgat A, Axelsen KB, Muthukrishnan V, Coudert E, Aimo L, Hyka-Nouspikel N, Gasteiger E, Kerhornou A, Neto TB, Pozzato M, Blatter MC, Ignatchenko A, Redaschi N, Bridge A: Rhea, the reaction knowledgebase in 2022. Nucleic Acids Res. 2022 Jan 7;50(D1):D693-D700. doi: 10.1093/nar/gkab1016. [PubMed:34755880 ]

Showing metabocard for (+)-copalyl diphosphate (MMDBc0054018)

MOL for #<Metabolite:0x00007fa4a28d0380>

3D MOL for #<Metabolite:0x00007fa4a28d0380>

3D SDF for #<Metabolite:0x00007fa4a28d0380>

3D-SDF for #<Metabolite:0x00007fa4a28d0380>

PDB for #<Metabolite:0x00007fa4a28d0380>

3D PDB for #<Metabolite:0x00007fa4a28d0380>

SMILES for #<Metabolite:0x00007fa4a28d0380>

INCHI for #<Metabolite:0x00007fa4a28d0380>

Structure for #<Metabolite:0x00007fa4a28d0380>

3D Structure for #<Metabolite:0x00007fa4a28d0380>