NP-MRD: Showing NP-Card for precorrin-1 (NP0300878)

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Record Information

Version

2.0

Created at

2022-09-10 13:31:44 UTC

Updated at

2022-09-10 13:31:44 UTC

NP-MRD ID

NP0300878

Secondary Accession Numbers

None

Natural Product Identification

Common Name

precorrin-1

Description

Precorrin-1 belongs to the class of organic compounds known as tetrapyrroles and derivatives. These are polycyclic aromatic compounds containing four pyrrole rings joined by one-carbon units linking position 2 of one pyrrole ring to position 5 of the next. Precorrin-1 is a weakly acidic compound (based on its pKa). Precorrin-1 exists in both E. Coli (prokaryote) and yeast (eukaryote).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv0541 02241222012D          

 61 65  0  0  1  0            999 V2000
    9.9852   -4.7163    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.2544   -4.3253    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
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    8.6573   -4.9051    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    9.2647   -3.5017    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    7.8305   -4.9016    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   12.1810   -4.3219    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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  1  2  1  0  0  0  0
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  1  4  2  0  0  0  0
  2  5  1  0  0  0  0
  2  6  1  6  0  0  0
  3  7  1  0  0  0  0
  4  8  1  0  0  0  0
  5  9  1  1  0  0  0
  5 10  1  6  0  0  0
  6 11  1  0  0  0  0
  7 12  2  0  0  0  0
  7 13  1  0  0  0  0
  8 14  2  0  0  0  0
  9 15  1  0  0  0  0
 11 16  1  0  0  0  0
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 12 18  1  0  0  0  0
 13 19  1  0  0  0  0
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M  END

     RDKit          3D

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M  END


  Mrv0541 02241222012D          

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M  END
> <DATABASE_ID>
NP0300878

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@]1(CC(O)=O)[C@H](CCC(O)=O)C2=N\C1=C/C1=C(CC(O)=O)C(CCC(O)=O)=C(CC3=C(CCC(O)=O)C(CC(O)=O)=C(CC4=C(CCC(O)=O)C(CC(O)=O)=C(C2)N4)N3)N1

> <INCHI_IDENTIFIER>
InChI=1S/C41H46N4O16/c1-41(17-40(60)61)24(5-9-36(52)53)31-15-29-22(11-38(56)57)19(3-7-34(48)49)27(43-29)14-28-21(10-37(54)55)18(2-6-33(46)47)25(42-28)13-26-20(4-8-35(50)51)23(12-39(58)59)30(44-26)16-32(41)45-31/h16,24,42-44H,2-15,17H2,1H3,(H,46,47)(H,48,49)(H,50,51)(H,52,53)(H,54,55)(H,56,57)(H,58,59)(H,60,61)/b32-16-/t24-,41+/m1/s1

> <INCHI_KEY>
CJLVUWULFKHGFB-NZCAJUPMSA-N

> <FORMULA>
C41H46N4O16

> <MOLECULAR_WEIGHT>
850.8211

> <EXACT_MASS>
850.290881444

> <JCHEM_ACCEPTOR_COUNT>
17

> <JCHEM_AVERAGE_POLARIZABILITY>
85.29404408948

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
11

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3-[(4S,5S)-10,14,19-tris(2-carboxyethyl)-5,9,15,20-tetrakis(carboxymethyl)-5-methyl-21,22,23,24-tetraazapentacyclo[16.2.1.1³,⁶.1⁸,¹¹.1¹³,¹⁶]tetracosa-1(20),3(24),6,8,10,13,15,18-octaen-4-yl]propanoic acid

> <ALOGPS_LOGP>
0.82

> <JCHEM_LOGP>
1.5674665769999998

> <ALOGPS_LOGS>
-4.30

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-8

> <JCHEM_PKA>
3.54907401394642

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.1769468444117646

> <JCHEM_POLAR_SURFACE_AREA>
358.12999999999994

> <JCHEM_REFRACTIVITY>
211.01020000000017

> <JCHEM_ROTATABLE_BOND_COUNT>
20

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
4.31e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-[(4S,5S)-10,14,19-tris(2-carboxyethyl)-5,9,15,20-tetrakis(carboxymethyl)-5-methyl-21,22,23,24-tetraazapentacyclo[16.2.1.1³,⁶.1⁸,¹¹.1¹³,¹⁶]tetracosa-1(20),3(24),6,8,10,13,15,18-octaen-4-yl]propanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  C   UNK     0      18.639  -8.804   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      17.275  -8.074   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      20.042  -8.279   0.000  0.00  0.00           C+0
HETATM    4  N   UNK     0      18.389 -10.315   0.000  0.00  0.00           N+0
HETATM    5  C   UNK     0      16.160  -9.156   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      17.294  -6.537   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      21.412  -8.855   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      16.865 -10.552   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      14.617  -9.150   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      15.584  -7.734   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      15.968  -5.762   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      22.738  -8.068   0.000  0.00  0.00           C+0
HETATM   13  N   UNK     0      21.739 -10.360   0.000  0.00  0.00           N+0
HETATM   14  C   UNK     0      16.128 -11.968   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      13.861  -7.811   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      15.987  -4.218   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      23.891  -9.092   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      22.732  -6.511   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      23.269 -10.501   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      16.865 -13.377   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0      12.324  -7.798   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0      14.636  -6.479   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0      14.668  -3.437   0.000  0.00  0.00           O+0
HETATM   24  O   UNK     0      17.326  -3.463   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0      25.428  -9.086   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      24.064  -5.743   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      23.846 -11.929   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      16.160 -14.760   0.000  0.00  0.00           C+0
HETATM   29  N   UNK     0      18.383 -13.601   0.000  0.00  0.00           N+0
HETATM   30  C   UNK     0      26.184  -7.747   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0      24.064  -4.205   0.000  0.00  0.00           O+0
HETATM   32  O   UNK     0      25.402  -6.505   0.000  0.00  0.00           O+0
HETATM   33  C   UNK     0      23.231 -13.351   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0      17.268 -15.823   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0      14.649 -15.010   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0      18.633 -15.125   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0      27.727  -7.734   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0      23.897 -14.754   0.000  0.00  0.00           C+0
HETATM   39  N   UNK     0      21.707 -13.562   0.000  0.00  0.00           N+0
HETATM   40  C   UNK     0      17.256 -17.367   0.000  0.00  0.00           C+0
HETATM   41  C   UNK     0      14.111 -16.444   0.000  0.00  0.00           C+0
HETATM   42  C   UNK     0      20.042 -15.650   0.000  0.00  0.00           C+0
HETATM   43  O   UNK     0      28.489  -6.396   0.000  0.00  0.00           O+0
HETATM   44  O   UNK     0      28.508  -9.066   0.000  0.00  0.00           O+0
HETATM   45  C   UNK     0      22.776 -15.798   0.000  0.00  0.00           C+0
HETATM   46  C   UNK     0      25.383 -14.344   0.000  0.00  0.00           C+0
HETATM   47  C   UNK     0      21.425 -15.074   0.000  0.00  0.00           C+0
HETATM   48  C   UNK     0      15.904 -18.142   0.000  0.00  0.00           C+0
HETATM   49  O   UNK     0      12.599 -16.701   0.000  0.00  0.00           O+0
HETATM   50  O   UNK     0      15.085 -17.629   0.000  0.00  0.00           O+0
HETATM   51  C   UNK     0      22.924 -17.328   0.000  0.00  0.00           C+0
HETATM   52  C   UNK     0      26.472 -15.420   0.000  0.00  0.00           C+0
HETATM   53  C   UNK     0      15.898 -19.692   0.000  0.00  0.00           C+0
HETATM   54  C   UNK     0      24.333 -17.969   0.000  0.00  0.00           C+0
HETATM   55  O   UNK     0      27.958 -15.016   0.000  0.00  0.00           O+0
HETATM   56  O   UNK     0      26.088 -16.912   0.000  0.00  0.00           O+0
HETATM   57  O   UNK     0      14.572 -20.447   0.000  0.00  0.00           O+0
HETATM   58  O   UNK     0      17.224 -20.460   0.000  0.00  0.00           O+0
HETATM   59  C   UNK     0      24.473 -19.506   0.000  0.00  0.00           C+0
HETATM   60  O   UNK     0      23.212 -20.390   0.000  0.00  0.00           O+0
HETATM   61  O   UNK     0      25.889 -20.140   0.000  0.00  0.00           O+0
CONECT    1    2    3    4                                                  
CONECT    2    1    5    6                                                  
CONECT    3    1    7                                                       
CONECT    4    1    8                                                       
CONECT    5    2    9   10    8                                             
CONECT    6    2   11                                                       
CONECT    7    3   12   13                                                  
CONECT    8    4   14    5                                                  
CONECT    9    5   15                                                       
CONECT   10    5                                                            
CONECT   11    6   16                                                       
CONECT   12    7   17   18                                                  
CONECT   13    7   19                                                       
CONECT   14    8   20                                                       
CONECT   15    9   21   22                                                  
CONECT   16   11   23   24                                                  
CONECT   17   12   25   19                                                  
CONECT   18   12   26                                                       
CONECT   19   13   27   17                                                  
CONECT   20   14   28   29                                                  
CONECT   21   15                                                            
CONECT   22   15                                                            
CONECT   23   16                                                            
CONECT   24   16                                                            
CONECT   25   17   30                                                       
CONECT   26   18   31   32                                                  
CONECT   27   19   33                                                       
CONECT   28   20   34   35                                                  
CONECT   29   20   36                                                       
CONECT   30   25   37                                                       
CONECT   31   26                                                            
CONECT   32   26                                                            
CONECT   33   27   38   39                                                  
CONECT   34   28   40   36                                                  
CONECT   35   28   41                                                       
CONECT   36   29   42   34                                                  
CONECT   37   30   43   44                                                  
CONECT   38   33   45   46                                                  
CONECT   39   33   47                                                       
CONECT   40   34   48                                                       
CONECT   41   35   49   50                                                  
CONECT   42   36   47                                                       
CONECT   43   37                                                            
CONECT   44   37                                                            
CONECT   45   38   51   47                                                  
CONECT   46   38   52                                                       
CONECT   47   39   42   45                                                  
CONECT   48   40   53                                                       
CONECT   49   41                                                            
CONECT   50   41                                                            
CONECT   51   45   54                                                       
CONECT   52   46   55   56                                                  
CONECT   53   48   57   58                                                  
CONECT   54   51   59                                                       
CONECT   55   52                                                            
CONECT   56   52                                                            
CONECT   57   53                                                            
CONECT   58   53                                                            
CONECT   59   54   60   61                                                  
CONECT   60   59                                                            
CONECT   61   59                                                            
MASTER        0    0    0    0    0    0    0    0   61    0  130    0
END

View in JSmol

Synonyms

Value	Source
Precorrin 1	ChEBI

Chemical Formula

C₄₁H₄₆N₄O₁₆

Average Mass

850.8211 Da

Monoisotopic Mass

850.29088 Da

IUPAC Name

3-[(4S,5S)-10,14,19-tris(2-carboxyethyl)-5,9,15,20-tetrakis(carboxymethyl)-5-methyl-21,22,23,24-tetraazapentacyclo[16.2.1.1³,⁶.1⁸,¹¹.1¹³,¹⁶]tetracosa-1(20),3(24),6,8,10,13,15,18-octaen-4-yl]propanoic acid

Traditional Name

CAS Registry Number

Not Available

SMILES

C[C@]1(CC(O)=O)[C@H](CCC(O)=O)C2=N\C1=C/C1=C(CC(O)=O)C(CCC(O)=O)=C(CC3=C(CCC(O)=O)C(CC(O)=O)=C(CC4=C(CCC(O)=O)C(CC(O)=O)=C(C2)N4)N3)N1

InChI Identifier

InChI=1S/C41H46N4O16/c1-41(17-40(60)61)24(5-9-36(52)53)31-15-29-22(11-38(56)57)19(3-7-34(48)49)27(43-29)14-28-21(10-37(54)55)18(2-6-33(46)47)25(42-28)13-26-20(4-8-35(50)51)23(12-39(58)59)30(44-26)16-32(41)45-31/h16,24,42-44H,2-15,17H2,1H3,(H,46,47)(H,48,49)(H,50,51)(H,52,53)(H,54,55)(H,56,57)(H,58,59)(H,60,61)/b32-16-/t24-,41+/m1/s1

InChI Key

CJLVUWULFKHGFB-NZCAJUPMSA-N

Experimental Spectra

Not Available

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 25 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Not Available

Species

Species of Origin

Not Available

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as tetrapyrroles and derivatives. These are polycyclic aromatic compounds containing four pyrrole rings joined by one-carbon units linking position 2 of one pyrrole ring to position 5 of the next.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Tetrapyrroles and derivatives

Sub Class

Not Available

Direct Parent

Tetrapyrroles and derivatives

Alternative Parents

Substituents

Tetrapyrrole skeleton
Substituted pyrrole
Pyrrole
Pyrroline
Heteroaromatic compound
Ketimine
Carboxylic acid derivative
Azacycle
Organic 1,3-dipolar compound
Propargyl-type 1,3-dipolar organic compound
Carboxylic acid
Organic oxygen compound
Organic nitrogen compound
Carbonyl group
Organooxygen compound
Organonitrogen compound
Imine
Hydrocarbon derivative
Organic oxide
Organopnictogen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

precorrin (CHEBI:52469 )

Physical Properties

State

Not Available

Experimental Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Predicted Properties

Property	Value	Source
logP	0.82	ALOGPS
logP	1.57	ChemAxon
logS	-4.3	ALOGPS
pKa (Strongest Acidic)	3.18	ChemAxon
Physiological Charge	-8	ChemAxon
Hydrogen Acceptor Count	17	ChemAxon
Hydrogen Donor Count	11	ChemAxon
Polar Surface Area	358.13 Å²	ChemAxon
Rotatable Bond Count	20	ChemAxon
Refractivity	211.01 m³·mol⁻¹	ChemAxon
Polarizability	85.29 Å³	ChemAxon
Number of Rings	5	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	ChemAxon

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

C15527

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

11954200

PDB ID

Not Available

ChEBI ID

52469

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for precorrin-1 (NP0300878)

MOL for NP0300878 (precorrin-1)

3D MOL for NP0300878 (precorrin-1)

3D SDF for NP0300878 (precorrin-1)

3D-SDF for NP0300878 (precorrin-1)

PDB for NP0300878 (precorrin-1)

3D PDB for NP0300878 (precorrin-1)

SMILES for NP0300878 (precorrin-1)

INCHI for NP0300878 (precorrin-1)

Structure for NP0300878 (precorrin-1)

3D Structure for NP0300878 (precorrin-1)