NP-MRD: Showing NP-Card for Rubrifacine (NP0008212)

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Record Information

Version

1.0

Created at

2020-12-09 05:51:46 UTC

Updated at

2021-07-15 16:59:45 UTC

NP-MRD ID

NP0008212

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Rubrifacine

Provided By

NPAtlas

Description

Rubrifacine is found in Brenneria rubrifaciens. It was first documented in 2002 (PMID: 28267306). Based on a literature review a small amount of articles have been published on Rubrifacine (PMID: 19159306) (PMID: 26389440) (PMID: 26389428) (PMID: 26389376).

Structure

MOL 3D MOL SDF 3D SDF PDB SMILES InChI


  Mrv1652306242106083D          

 34 35  0  0  0  0            999 V2000
    1.3884    1.8279    2.6387 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1744    0.9263    2.2818 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4868    1.0690    2.7998 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8399   -0.2191    1.4019 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.6938    0.1245   -0.0151 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6333   -0.0903   -0.8110 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6303   -0.7216   -0.4604 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8342   -0.0753   -0.5921 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9055    1.3522   -1.0143 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.5810    2.2648    0.1061 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3216    1.7829    1.2207 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5639    3.6260   -0.0713 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0157   -0.7164   -0.3005 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0611   -1.9784    0.1203 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1567   -2.5714    0.3909 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8884   -2.6790    0.2730 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9452   -3.9969    0.7142 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6735   -2.0487   -0.0187 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4510   -2.7818    0.1414 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9171    0.3759   -2.1254 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.2260    0.9128   -2.1458 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8199    1.4233   -3.1472 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7504    0.7652   -0.8025 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9011    1.1358   -0.4415 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.0699    1.6855    2.2460 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8890   -0.6445    1.8181 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6202   -1.0120    1.4914 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9736    1.5677   -1.3013 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2098    1.5667   -1.8134 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7819    4.1447   -0.4389 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9181   -0.1893   -0.4141 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1032   -4.5580    0.8450 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4021   -2.6062   -0.0062 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3004    0.3380   -2.9923 H   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
  2  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  2  0  0  0  0
 10 12  1  0  0  0  0
  8 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  2  0  0  0  0
 14 16  1  0  0  0  0
 16 17  1  0  0  0  0
 16 18  2  0  0  0  0
 18 19  1  0  0  0  0
  6 20  1  0  0  0  0
 20 21  1  0  0  0  0
 21 22  2  0  0  0  0
 21 23  1  0  0  0  0
 23 24  2  0  0  0  0
 23  5  1  0  0  0  0
 18  7  1  0  0  0  0
  3 25  1  0  0  0  0
  4 26  1  0  0  0  0
  4 27  1  0  0  0  0
  9 28  1  0  0  0  0
  9 29  1  0  0  0  0
 12 30  1  0  0  0  0
 13 31  1  0  0  0  0
 17 32  1  0  0  0  0
 19 33  1  0  0  0  0
 20 34  1  0  0  0  0
M  END

     RDKit          3D

 34 35  0  0  0  0  0  0  0  0999 V2000
    1.3884    1.8279    2.6387 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1744    0.9263    2.2818 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4868    1.0690    2.7998 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8399   -0.2191    1.4019 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6938    0.1245   -0.0151 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6333   -0.0903   -0.8110 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6303   -0.7216   -0.4604 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8342   -0.0753   -0.5921 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9055    1.3522   -1.0143 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5810    2.2648    0.1061 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3216    1.7829    1.2207 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5639    3.6260   -0.0713 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0157   -0.7164   -0.3005 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0611   -1.9784    0.1203 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1567   -2.5714    0.3909 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8884   -2.6790    0.2730 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9452   -3.9969    0.7142 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6735   -2.0487   -0.0187 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4510   -2.7818    0.1414 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9171    0.3759   -2.1254 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.2260    0.9128   -2.1458 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8199    1.4233   -3.1472 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7504    0.7652   -0.8025 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9011    1.1358   -0.4415 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.0699    1.6855    2.2460 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8890   -0.6445    1.8181 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6202   -1.0120    1.4914 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9736    1.5677   -1.3013 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2098    1.5667   -1.8134 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7819    4.1447   -0.4389 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9181   -0.1893   -0.4141 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1032   -4.5580    0.8450 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4021   -2.6062   -0.0062 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3004    0.3380   -2.9923 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  2  0
  8  9  1  0
  9 10  1  0
 10 11  2  0
 10 12  1  0
  8 13  1  0
 13 14  1  0
 14 15  2  0
 14 16  1  0
 16 17  1  0
 16 18  2  0
 18 19  1  0
  6 20  1  0
 20 21  1  0
 21 22  2  0
 21 23  1  0
 23 24  2  0
 23  5  1  0
 18  7  1  0
  3 25  1  0
  4 26  1  0
  4 27  1  0
  9 28  1  0
  9 29  1  0
 12 30  1  0
 13 31  1  0
 17 32  1  0
 19 33  1  0
 20 34  1  0
M  END


  Mrv1652306242106083D          

 34 35  0  0  0  0            999 V2000
    1.3884    1.8279    2.6387 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1744    0.9263    2.2818 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4868    1.0690    2.7998 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8399   -0.2191    1.4019 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.6938    0.1245   -0.0151 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6333   -0.0903   -0.8110 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6303   -0.7216   -0.4604 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8342   -0.0753   -0.5921 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9055    1.3522   -1.0143 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.5810    2.2648    0.1061 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3216    1.7829    1.2207 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5639    3.6260   -0.0713 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0157   -0.7164   -0.3005 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0611   -1.9784    0.1203 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1567   -2.5714    0.3909 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8884   -2.6790    0.2730 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9452   -3.9969    0.7142 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6735   -2.0487   -0.0187 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4510   -2.7818    0.1414 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9171    0.3759   -2.1254 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.2260    0.9128   -2.1458 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8199    1.4233   -3.1472 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7504    0.7652   -0.8025 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9011    1.1358   -0.4415 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.0699    1.6855    2.2460 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8890   -0.6445    1.8181 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6202   -1.0120    1.4914 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9736    1.5677   -1.3013 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2098    1.5667   -1.8134 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7819    4.1447   -0.4389 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9181   -0.1893   -0.4141 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1032   -4.5580    0.8450 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4021   -2.6062   -0.0062 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3004    0.3380   -2.9923 H   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
  2  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  2  0  0  0  0
 10 12  1  0  0  0  0
  8 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  2  0  0  0  0
 14 16  1  0  0  0  0
 16 17  1  0  0  0  0
 16 18  2  0  0  0  0
 18 19  1  0  0  0  0
  6 20  1  0  0  0  0
 20 21  1  0  0  0  0
 21 22  2  0  0  0  0
 21 23  1  0  0  0  0
 23 24  2  0  0  0  0
 23  5  1  0  0  0  0
 18  7  1  0  0  0  0
  3 25  1  0  0  0  0
  4 26  1  0  0  0  0
  4 27  1  0  0  0  0
  9 28  1  0  0  0  0
  9 29  1  0  0  0  0
 12 30  1  0  0  0  0
 13 31  1  0  0  0  0
 17 32  1  0  0  0  0
 19 33  1  0  0  0  0
 20 34  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0008212

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H]OC(=O)C([H])([H])C1=C(N([H])C(=O)C1=O)C1=C(N([H])C(=O)C(O[H])=C1O[H])C([H])([H])C(=O)O[H]

> <INCHI_IDENTIFIER>
InChI=1S/C13H10N2O9/c16-5(17)1-3-8(15-12(23)9(3)20)7-4(2-6(18)19)14-13(24)11(22)10(7)21/h22H,1-2H2,(H,16,17)(H,18,19)(H2,14,21,24)(H,15,20,23)

> <INCHI_KEY>
NHGFIXIYKNHGSJ-UHFFFAOYSA-N

> <FORMULA>
C13H10N2O9

> <MOLECULAR_WEIGHT>
338.228

> <EXACT_MASS>
338.03862991

> <JCHEM_ACCEPTOR_COUNT>
9

> <JCHEM_ATOM_COUNT>
34

> <JCHEM_AVERAGE_POLARIZABILITY>
28.60905035000023

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-{2-[2-(carboxymethyl)-4,5-dihydroxy-6-oxo-1,6-dihydropyridin-3-yl]-4,5-dioxo-4,5-dihydro-1H-pyrrol-3-yl}acetic acid

> <ALOGPS_LOGP>
-0.81

> <JCHEM_LOGP>
-2.7153733216666662

> <ALOGPS_LOGS>
-3.08

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-3

> <JCHEM_PKA>
3.96202086404272

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.29398831024219

> <JCHEM_PKA_STRONGEST_BASIC>
-4.6285764601564

> <JCHEM_POLAR_SURFACE_AREA>
190.32999999999998

> <JCHEM_REFRACTIVITY>
76.32159999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
2.81e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
{2-[2-(carboxymethyl)-4,5-dihydroxy-6-oxo-1H-pyridin-3-yl]-4,5-dioxo-1H-pyrrol-3-yl}acetic acid

> <JCHEM_VEBER_RULE>
0

$$$$

     RDKit          3D

 34 35  0  0  0  0  0  0  0  0999 V2000
    1.3884    1.8279    2.6387 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1744    0.9263    2.2818 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4868    1.0690    2.7998 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8399   -0.2191    1.4019 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6938    0.1245   -0.0151 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6333   -0.0903   -0.8110 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6303   -0.7216   -0.4604 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8342   -0.0753   -0.5921 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9055    1.3522   -1.0143 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5810    2.2648    0.1061 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3216    1.7829    1.2207 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5639    3.6260   -0.0713 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0157   -0.7164   -0.3005 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0611   -1.9784    0.1203 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1567   -2.5714    0.3909 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8884   -2.6790    0.2730 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9452   -3.9969    0.7142 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6735   -2.0487   -0.0187 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4510   -2.7818    0.1414 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9171    0.3759   -2.1254 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.2260    0.9128   -2.1458 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8199    1.4233   -3.1472 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7504    0.7652   -0.8025 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9011    1.1358   -0.4415 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.0699    1.6855    2.2460 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8890   -0.6445    1.8181 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6202   -1.0120    1.4914 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9736    1.5677   -1.3013 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2098    1.5667   -1.8134 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7819    4.1447   -0.4389 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9181   -0.1893   -0.4141 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1032   -4.5580    0.8450 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4021   -2.6062   -0.0062 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3004    0.3380   -2.9923 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  2  0
  8  9  1  0
  9 10  1  0
 10 11  2  0
 10 12  1  0
  8 13  1  0
 13 14  1  0
 14 15  2  0
 14 16  1  0
 16 17  1  0
 16 18  2  0
 18 19  1  0
  6 20  1  0
 20 21  1  0
 21 22  2  0
 21 23  1  0
 23 24  2  0
 23  5  1  0
 18  7  1  0
  3 25  1  0
  4 26  1  0
  4 27  1  0
  9 28  1  0
  9 29  1  0
 12 30  1  0
 13 31  1  0
 17 32  1  0
 19 33  1  0
 20 34  1  0
M  END

HEADER    PROTEIN                                 24-JUN-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-JUN-21         0                                  
HETATM    1  O   UNK     0       1.388   1.828   2.639  0.00  0.00           O+0
HETATM    2  C   UNK     0       2.174   0.926   2.282  0.00  0.00           C+0
HETATM    3  O   UNK     0       3.487   1.069   2.800  0.00  0.00           O+0
HETATM    4  C   UNK     0       1.840  -0.219   1.402  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.694   0.125  -0.015  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.633  -0.090  -0.811  0.00  0.00           C+0
HETATM    7  C   UNK     0      -0.630  -0.722  -0.460  0.00  0.00           C+0
HETATM    8  C   UNK     0      -1.834  -0.075  -0.592  0.00  0.00           C+0
HETATM    9  C   UNK     0      -1.906   1.352  -1.014  0.00  0.00           C+0
HETATM   10  C   UNK     0      -1.581   2.265   0.106  0.00  0.00           C+0
HETATM   11  O   UNK     0      -1.322   1.783   1.221  0.00  0.00           O+0
HETATM   12  O   UNK     0      -1.564   3.626  -0.071  0.00  0.00           O+0
HETATM   13  N   UNK     0      -3.016  -0.716  -0.301  0.00  0.00           N+0
HETATM   14  C   UNK     0      -3.061  -1.978   0.120  0.00  0.00           C+0
HETATM   15  O   UNK     0      -4.157  -2.571   0.391  0.00  0.00           O+0
HETATM   16  C   UNK     0      -1.888  -2.679   0.273  0.00  0.00           C+0
HETATM   17  O   UNK     0      -1.945  -3.997   0.714  0.00  0.00           O+0
HETATM   18  C   UNK     0      -0.674  -2.049  -0.019  0.00  0.00           C+0
HETATM   19  O   UNK     0       0.451  -2.782   0.141  0.00  0.00           O+0
HETATM   20  N   UNK     0       0.917   0.376  -2.125  0.00  0.00           N+0
HETATM   21  C   UNK     0       2.226   0.913  -2.146  0.00  0.00           C+0
HETATM   22  O   UNK     0       2.820   1.423  -3.147  0.00  0.00           O+0
HETATM   23  C   UNK     0       2.750   0.765  -0.803  0.00  0.00           C+0
HETATM   24  O   UNK     0       3.901   1.136  -0.442  0.00  0.00           O+0
HETATM   25  H   UNK     0       4.070   1.686   2.246  0.00  0.00           H+0
HETATM   26  H   UNK     0       0.889  -0.645   1.818  0.00  0.00           H+0
HETATM   27  H   UNK     0       2.620  -1.012   1.491  0.00  0.00           H+0
HETATM   28  H   UNK     0      -2.974   1.568  -1.301  0.00  0.00           H+0
HETATM   29  H   UNK     0      -1.210   1.567  -1.813  0.00  0.00           H+0
HETATM   30  H   UNK     0      -0.782   4.145  -0.439  0.00  0.00           H+0
HETATM   31  H   UNK     0      -3.918  -0.189  -0.414  0.00  0.00           H+0
HETATM   32  H   UNK     0      -1.103  -4.558   0.845  0.00  0.00           H+0
HETATM   33  H   UNK     0       1.402  -2.606  -0.006  0.00  0.00           H+0
HETATM   34  H   UNK     0       0.300   0.338  -2.992  0.00  0.00           H+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2   25                                                       
CONECT    4    2    5   26   27                                             
CONECT    5    4    6   23                                                  
CONECT    6    5    7   20                                                  
CONECT    7    6    8   18                                                  
CONECT    8    7    9   13                                                  
CONECT    9    8   10   28   29                                             
CONECT   10    9   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10   30                                                       
CONECT   13    8   14   31                                                  
CONECT   14   13   15   16                                                  
CONECT   15   14                                                            
CONECT   16   14   17   18                                                  
CONECT   17   16   32                                                       
CONECT   18   16   19    7                                                  
CONECT   19   18   33                                                       
CONECT   20    6   21   34                                                  
CONECT   21   20   22   23                                                  
CONECT   22   21                                                            
CONECT   23   21   24    5                                                  
CONECT   24   23                                                            
CONECT   25    3                                                            
CONECT   26    4                                                            
CONECT   27    4                                                            
CONECT   28    9                                                            
CONECT   29    9                                                            
CONECT   30   12                                                            
CONECT   31   13                                                            
CONECT   32   17                                                            
CONECT   33   19                                                            
CONECT   34   20                                                            
MASTER        0    0    0    0    0    0    0    0   34    0   70    0
END

RDKit          3D

34 35  0  0  0  0  0  0  0  0999 V2000
    1.3884    1.8279    2.6387 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1744    0.9263    2.2818 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4868    1.0690    2.7998 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8399   -0.2191    1.4019 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6938    0.1245   -0.0151 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6333   -0.0903   -0.8110 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6303   -0.7216   -0.4604 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8342   -0.0753   -0.5921 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9055    1.3522   -1.0143 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5810    2.2648    0.1061 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3216    1.7829    1.2207 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5639    3.6260   -0.0713 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0157   -0.7164   -0.3005 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0611   -1.9784    0.1203 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1567   -2.5714    0.3909 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8884   -2.6790    0.2730 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9452   -3.9969    0.7142 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6735   -2.0487   -0.0187 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4510   -2.7818    0.1414 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9171    0.3759   -2.1254 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.2260    0.9128   -2.1458 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8199    1.4233   -3.1472 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7504    0.7652   -0.8025 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9011    1.1358   -0.4415 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.0699    1.6855    2.2460 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8890   -0.6445    1.8181 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6202   -1.0120    1.4914 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9736    1.5677   -1.3013 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2098    1.5667   -1.8134 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7819    4.1447   -0.4389 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9181   -0.1893   -0.4141 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1032   -4.5580    0.8450 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4021   -2.6062   -0.0062 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3004    0.3380   -2.9923 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  2  0
  8  9  1  0
  9 10  1  0
 10 11  2  0
 10 12  1  0
  8 13  1  0
 13 14  1  0
 14 15  2  0
 14 16  1  0
 16 17  1  0
 16 18  2  0
 18 19  1  0
  6 20  1  0
 20 21  1  0
 21 22  2  0
 21 23  1  0
 23 24  2  0
 23  5  1  0
 18  7  1  0
  3 25  1  0
  4 26  1  0
  4 27  1  0
  9 28  1  0
  9 29  1  0
 12 30  1  0
 13 31  1  0
 17 32  1  0
 19 33  1  0
 20 34  1  0
M  END

View in JSmol View NMR Assignments

Synonyms

Value	Source
3-(3-Carboxymethyl-4,5-dihydro-4,5-dioxo-2-pyrrolyl)-4,5,6-trihydroxy-pyridine-2-acetic acid	MeSH
3-(3-Carboxymethyl-4,5-dihydro-4,5-dioxo-2-pyrrolyl)-4,5,6-trihydroxy-pyridine-2-acetate	Generator
Rubrifacine	MeSH
2-{2-[2-(carboxymethyl)-4,5,6-trihydroxypyridin-3-yl]-4,5-dioxo-4,5-dihydro-1H-pyrrol-3-yl}acetate	Generator

Chemical Formula

C₁₃H₁₀N₂O₉

Average Mass

338.2280 Da

Monoisotopic Mass

338.03863 Da

IUPAC Name

2-{2-[2-(carboxymethyl)-4,5-dihydroxy-6-oxo-1,6-dihydropyridin-3-yl]-4,5-dioxo-4,5-dihydro-1H-pyrrol-3-yl}acetic acid

Traditional Name

{2-[2-(carboxymethyl)-4,5-dihydroxy-6-oxo-1H-pyridin-3-yl]-4,5-dioxo-1H-pyrrol-3-yl}acetic acid

CAS Registry Number

Not Available

SMILES

OC(=O)CC1=C(NC(=O)C1=O)C1=C(CC(O)=O)NC(=O)C(O)=C1O

InChI Identifier

InChI=1S/C13H10N2O9/c16-5(17)1-3-8(15-12(23)9(3)20)7-4(2-6(18)19)14-13(24)11(22)10(7)21/h22H,1-2H2,(H,16,17)(H,18,19)(H2,14,21,24)(H,15,20,23)

InChI Key

NHGFIXIYKNHGSJ-UHFFFAOYSA-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, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Brenneria rubrifaciens	NPAtlas	19159306

Chemical Taxonomy

Description

This compound belongs to the class of organic compounds known as pyridinones. These are compounds containing a pyridine ring, which bears a ketone.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Pyridines and derivatives

Sub Class

Hydropyridines

Direct Parent

Pyridinones

Alternative Parents

Substituents

Dihydropyridine
Pyridinone
Hydroxypyridine
Dicarboxylic acid or derivatives
Pyrroline
Vinylogous acid
Vinylogous amide
Heteroaromatic compound
Carboxamide group
Ketone
Cyclic ketone
Secondary carboxylic acid amide
Lactam
Carboxylic acid derivative
Azacycle
Carboxylic acid
Carbonyl group
Organic oxygen compound
Organic nitrogen compound
Organic oxide
Hydrocarbon derivative
Organonitrogen compound
Organooxygen compound
Organopnictogen compound
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

Not Available

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	-0.81	ALOGPS
logP	-2.7	ChemAxon
logS	-3.1	ALOGPS
pKa (Strongest Acidic)	3.29	ChemAxon
pKa (Strongest Basic)	-4.6	ChemAxon
Physiological Charge	-3	ChemAxon
Hydrogen Acceptor Count	9	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	190.33 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	76.32 m³·mol⁻¹	ChemAxon
Polarizability	28.61 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

NPAtlas ID

NPA019118

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

67156295

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

129674665

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

McClean AE, Kluepfel DA: Genetic loci involved in rubrifacine production in the walnut pathogen Brenneria rubrifaciens. Phytopathology. 2009 Feb;99(2):145-51. doi: 10.1094/PHYTO-99-2-0145. [PubMed:19159306 ]
Authors unspecified: Medicinal Mushrooms (PDQ(R)): Patient Version. 2002. [PubMed:28267306 ]
Authors unspecified: Nutrition in Cancer Care (PDQ(R)): Patient Version. 2002. [PubMed:26389440 ]
Authors unspecified: Lung Cancer Screening (PDQ(R)): Patient Version. 2002. [PubMed:26389428 ]
Authors unspecified: Colorectal Cancer Prevention (PDQ(R)): Patient Version. 2002. [PubMed:26389376 ]

Showing NP-Card for Rubrifacine (NP0008212)

MOL for NP0008212 (Rubrifacine)

3D MOL for NP0008212 (Rubrifacine)

3D SDF for NP0008212 (Rubrifacine)

3D-SDF for NP0008212 (Rubrifacine)

PDB for NP0008212 (Rubrifacine)

3D PDB for NP0008212 (Rubrifacine)

SMILES for NP0008212 (Rubrifacine)

INCHI for NP0008212 (Rubrifacine)

Structure for NP0008212 (Rubrifacine)

3D Structure for NP0008212 (Rubrifacine)