NP-MRD: Showing NP-Card for Puromycin (NP0050702)

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Record Information

Version

1.0

Created at

2022-04-27 22:02:45 UTC

Updated at

2022-04-27 22:02:45 UTC

NP-MRD ID

NP0050702

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Puromycin

Description

Puromycin is found in Streptomyces alboniger.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652304282200022D          

 34 37  0  0  1  0            999 V2000
    3.3523    1.9354    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523    1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    0.6979    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233    1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233    1.9354    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    2.3479    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    3.1729    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523    3.5854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233    3.5854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387    2.1904    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.6538    1.5229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387    0.8555    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.8838    0.0709    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.3687   -0.5966    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8838   -1.2640    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.0992   -1.0091    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.0992   -0.1841    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.5683    0.3009    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5683   -1.4940    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4820   -2.3145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2716   -2.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1495   -2.7994    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.0632   -3.6199    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3096   -3.9554    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3579   -3.4705    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1115   -3.8061    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1978   -4.6265    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5303   -5.1115    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2233   -4.7759    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9515   -4.9621    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6189   -4.4772    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9032   -2.4638    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387   -2.0486    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9457   -2.2201    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  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  1  0  0  0  0
  7  9  1  0  0  0  0
  5 10  1  0  0  0  0
 10 11  2  0  0  0  0
 11 12  1  0  0  0  0
  4 12  1  0  0  0  0
 13 12  1  6  0  0  0
 13 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
 13 17  1  0  0  0  0
 17 18  1  1  0  0  0
 16 19  1  6  0  0  0
 19 20  1  0  0  0  0
 20 21  2  0  0  0  0
 20 22  1  0  0  0  0
 22 23  1  0  0  0  0
 23 24  1  0  0  0  0
 24 25  2  0  0  0  0
 25 26  1  0  0  0  0
 26 27  2  0  0  0  0
 27 28  1  0  0  0  0
 28 29  2  0  0  0  0
 24 29  1  0  0  0  0
 27 30  1  0  0  0  0
 30 31  1  0  0  0  0
 22 32  1  1  0  0  0
 15 33  1  6  0  0  0
 33 34  1  0  0  0  0
M  END


  Mrv1652304282200022D          

 34 37  0  0  1  0            999 V2000
    3.3523    1.9354    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523    1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    0.6979    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233    1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233    1.9354    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    2.3479    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    3.1729    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523    3.5854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233    3.5854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387    2.1904    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.6538    1.5229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387    0.8555    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.8838    0.0709    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.3687   -0.5966    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8838   -1.2640    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.0992   -1.0091    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.0992   -0.1841    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.5683    0.3009    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5683   -1.4940    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4820   -2.3145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2716   -2.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1495   -2.7994    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.0632   -3.6199    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3096   -3.9554    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3579   -3.4705    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1115   -3.8061    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1978   -4.6265    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5303   -5.1115    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2233   -4.7759    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9515   -4.9621    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6189   -4.4772    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9032   -2.4638    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387   -2.0486    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9457   -2.2201    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  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  1  0  0  0  0
  7  9  1  0  0  0  0
  5 10  1  0  0  0  0
 10 11  2  0  0  0  0
 11 12  1  0  0  0  0
  4 12  1  0  0  0  0
 13 12  1  6  0  0  0
 13 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
 13 17  1  0  0  0  0
 17 18  1  1  0  0  0
 16 19  1  6  0  0  0
 19 20  1  0  0  0  0
 20 21  2  0  0  0  0
 20 22  1  0  0  0  0
 22 23  1  0  0  0  0
 23 24  1  0  0  0  0
 24 25  2  0  0  0  0
 25 26  1  0  0  0  0
 26 27  2  0  0  0  0
 27 28  1  0  0  0  0
 28 29  2  0  0  0  0
 24 29  1  0  0  0  0
 27 30  1  0  0  0  0
 30 31  1  0  0  0  0
 22 32  1  1  0  0  0
 15 33  1  6  0  0  0
 33 34  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0050702

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC1=CC=C(C[C@@H](N)C(=O)N[C@H]2[C@@H](CO)O[C@H]([C@@H]2O)N2C=NC3=C(N=CN=C23)N(C)C)C=C1

> <INCHI_IDENTIFIER>
InChI=1S/C22H29N7O5/c1-28(2)19-17-20(25-10-24-19)29(11-26-17)22-18(31)16(15(9-30)34-22)27-21(32)14(23)8-12-4-6-13(33-3)7-5-12/h4-7,10-11,14-16,18,22,30-31H,8-9,23H2,1-3H3,(H,27,32)/t14-,15-,16+,18-,22-/m1/s1

> <INCHI_KEY>
RXWNCPJZOCPEPQ-DYIOZPFISA-N

> <FORMULA>
C22H29N7O5

> <MOLECULAR_WEIGHT>
471.518

> <EXACT_MASS>
471.223017062

> <JCHEM_ACCEPTOR_COUNT>
10

> <JCHEM_ATOM_COUNT>
63

> <JCHEM_AVERAGE_POLARIZABILITY>
47.21455330027324

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(2R)-2-amino-N-[(2S,3R,4R,5R)-5-[6-(dimethylamino)-9H-purin-9-yl]-4-hydroxy-2-(hydroxymethyl)oxolan-3-yl]-3-(4-methoxyphenyl)propanamide

> <ALOGPS_LOGP>
-0.10

> <JCHEM_LOGP>
-0.29873975099999955

> <ALOGPS_LOGS>
-2.67

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
13.06459951728911

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.349177327822645

> <JCHEM_PKA_STRONGEST_BASIC>
8.032981412215106

> <JCHEM_POLAR_SURFACE_AREA>
160.88

> <JCHEM_REFRACTIVITY>
122.96089999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.01e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2R)-2-amino-N-[(2S,3R,4R,5R)-5-[6-(dimethylamino)purin-9-yl]-4-hydroxy-2-(hydroxymethyl)oxolan-3-yl]-3-(4-methoxyphenyl)propanamide

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 28-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   28-APR-22         0                                  
HETATM    1  N   UNK     0       6.258   3.613   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0       6.258   2.073   0.000  0.00  0.00           C+0
HETATM    3  N   UNK     0       4.924   1.303   0.000  0.00  0.00           N+0
HETATM    4  C   UNK     0       3.590   2.073   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       3.590   3.613   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       4.924   4.383   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0       4.924   5.923   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0       6.258   6.693   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       3.590   6.693   0.000  0.00  0.00           C+0
HETATM   10  N   UNK     0       2.126   4.089   0.000  0.00  0.00           N+0
HETATM   11  C   UNK     0       1.220   2.843   0.000  0.00  0.00           C+0
HETATM   12  N   UNK     0       2.126   1.597   0.000  0.00  0.00           N+0
HETATM   13  C   UNK     0       1.650   0.132   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0       2.555  -1.114   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0       1.650  -2.359   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       0.185  -1.884   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       0.185  -0.344   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0      -1.061   0.562   0.000  0.00  0.00           O+0
HETATM   19  N   UNK     0      -1.061  -2.789   0.000  0.00  0.00           N+0
HETATM   20  C   UNK     0      -0.900  -4.320   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0       0.507  -4.947   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0      -2.146  -5.226   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      -1.985  -6.757   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      -0.578  -7.383   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       0.668  -6.478   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       2.075  -7.105   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       2.236  -8.636   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       0.990  -9.541   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      -0.417  -8.915   0.000  0.00  0.00           C+0
HETATM   30  O   UNK     0       3.643  -9.263   0.000  0.00  0.00           O+0
HETATM   31  C   UNK     0       4.889  -8.357   0.000  0.00  0.00           C+0
HETATM   32  N   UNK     0      -3.553  -4.599   0.000  0.00  0.00           N+0
HETATM   33  C   UNK     0       2.126  -3.824   0.000  0.00  0.00           C+0
HETATM   34  O   UNK     0       3.632  -4.144   0.000  0.00  0.00           O+0
CONECT    1    2    6                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5   12                                                  
CONECT    5    4    6   10                                                  
CONECT    6    5    1    7                                                  
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7                                                            
CONECT   10    5   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11    4   13                                                  
CONECT   13   12   14   17                                                  
CONECT   14   13   15                                                       
CONECT   15   14   16   33                                                  
CONECT   16   15   17   19                                                  
CONECT   17   16   13   18                                                  
CONECT   18   17                                                            
CONECT   19   16   20                                                       
CONECT   20   19   21   22                                                  
CONECT   21   20                                                            
CONECT   22   20   23   32                                                  
CONECT   23   22   24                                                       
CONECT   24   23   25   29                                                  
CONECT   25   24   26                                                       
CONECT   26   25   27                                                       
CONECT   27   26   28   30                                                  
CONECT   28   27   29                                                       
CONECT   29   28   24                                                       
CONECT   30   27   31                                                       
CONECT   31   30                                                            
CONECT   32   22                                                            
CONECT   33   15   34                                                       
CONECT   34   33                                                            
MASTER        0    0    0    0    0    0    0    0   34    0   74    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₂H₂₉N₇O₅

Average Mass

471.5180 Da

Monoisotopic Mass

471.22302 Da

IUPAC Name

(2R)-2-amino-N-[(2S,3R,4R,5R)-5-[6-(dimethylamino)-9H-purin-9-yl]-4-hydroxy-2-(hydroxymethyl)oxolan-3-yl]-3-(4-methoxyphenyl)propanamide

Traditional Name

(2R)-2-amino-N-[(2S,3R,4R,5R)-5-[6-(dimethylamino)purin-9-yl]-4-hydroxy-2-(hydroxymethyl)oxolan-3-yl]-3-(4-methoxyphenyl)propanamide

CAS Registry Number

Not Available

SMILES

COC1=CC=C(C[C@@H](N)C(=O)N[C@H]2[C@@H](CO)O[C@H]([C@@H]2O)N2C=NC3=C(N=CN=C23)N(C)C)C=C1

InChI Identifier

InChI=1S/C22H29N7O5/c1-28(2)19-17-20(25-10-24-19)29(11-26-17)22-18(31)16(15(9-30)34-22)27-21(32)14(23)8-12-4-6-13(33-3)7-5-12/h4-7,10-11,14-16,18,22,30-31H,8-9,23H2,1-3H3,(H,27,32)/t14-,15-,16+,18-,22-/m1/s1

InChI Key

RXWNCPJZOCPEPQ-DYIOZPFISA-N

Experimental Spectra

Not Available

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Streptomyces alboniger	Bacteria	KNApSAcK

Chemical Taxonomy

Classification

Not classified

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	-0.1	ALOGPS
logP	-0.3	ChemAxon
logS	-2.7	ALOGPS
pKa (Strongest Acidic)	12.35	ChemAxon
pKa (Strongest Basic)	8.03	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	10	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	160.88 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	122.96 m³·mol⁻¹	ChemAxon
Polarizability	47.21 Å³	ChemAxon
Number of Rings	4	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	ChemAxon

External Links

Not Available

References

General References

Not Available

Showing NP-Card for Puromycin (NP0050702)

MOL for NP0050702 (Puromycin)

3D MOL for NP0050702 (Puromycin)

3D SDF for NP0050702 (Puromycin)

3D-SDF for NP0050702 (Puromycin)

PDB for NP0050702 (Puromycin)

3D PDB for NP0050702 (Puromycin)

SMILES for NP0050702 (Puromycin)

INCHI for NP0050702 (Puromycin)

Structure for NP0050702 (Puromycin)

3D Structure for NP0050702 (Puromycin)