Showing metabocard for 2,5-dihydroxypyridine (MMDBc0054205)

Record Information
Version2.0
StatusDetected and Quantified
Creation Date2022-06-05 22:58:39 UTC
Update Date2025-10-07 16:08:25 UTC
Metabolite IDMMDBc0054205
Metabolite Identification
Common Name2,5-dihydroxypyridine
Description2,5-dihydroxypyridine is a pyridine derivative and belongs to the class of heterocyclic organic compounds. Its chemical structure features a pyridine ring with hydroxyl groups at the 2 and 5 positions, which contributes to its reactivity and biological interactions. This compound is involved in various biochemical pathways, notably as a ligand for the NdpR protein, where it inhibits NdpR from binding to the promoter regions of genes such as ndpASAL, ndpTB, and ndpHFEGD (PMID:37071026 ). Additionally, 2,5-dihydroxypyridine serves as an effector molecule for NdpR, influencing its binding dynamics to DNA (PMID:37071026 ). The biodegradation of 2,5-dihydroxypyridine is catalyzed by 2,5-dihydroxypyridine dioxygenase (NicX) from Pseudomonas putida KT2440, which utilizes a mononuclear non-heme iron to cleave the pyridine ring, converting it into N-formylmaleamic acid (NFM) (PMID:36469460 , PMID:35060702 , PMID:33637718 ). The enzyme's activity is linked to the ocnE gene, which is essential for the function of the dioxygenase (PMID:32841574 ).
Structure
MOLSDFPDBSMILESInChI

MOL for #<Metabolite:0x0000564322f8b810>

 
  Mrv1533006041517292D          
 
  8  8  0  0  0  0            999 V2000
   12.2633   -9.8952    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.9683  -10.3114    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.2633   -9.0702    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.5545  -10.3002    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.6845   -9.8952    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.9683   -8.6614    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   13.6845   -9.0702    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.3895   -8.6614    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  1  3  1  0  0  0  0
  1  4  1  0  0  0  0
  2  5  1  0  0  0  0
  3  6  2  0  0  0  0
  5  7  2  0  0  0  0
  7  8  1  0  0  0  0
  6  7  1  0  0  0  0
M  END
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3D MOL for #<Metabolite:0x0000564322f8b810>

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3D SDF for #<Metabolite:0x0000564322f8b810>
 
  Mrv1533006041517292D          
 
  8  8  0  0  0  0            999 V2000
   12.2633   -9.8952    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.9683  -10.3114    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.2633   -9.0702    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.5545  -10.3002    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.6845   -9.8952    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.9683   -8.6614    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   13.6845   -9.0702    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.3895   -8.6614    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  1  3  1  0  0  0  0
  1  4  1  0  0  0  0
  2  5  1  0  0  0  0
  3  6  2  0  0  0  0
  5  7  2  0  0  0  0
  7  8  1  0  0  0  0
  6  7  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0054205

> <DATABASE_NAME>
MIME

> <SMILES>
OC1=CC=C(O)N=C1

> <INCHI_IDENTIFIER>
InChI=1S/C5H5NO2/c7-4-1-2-5(8)6-3-4/h1-3,7H,(H,6,8)

> <INCHI_KEY>
CHGPEDOMXOLANF-UHFFFAOYSA-N

> <FORMULA>
C5H5NO2

> <MOLECULAR_WEIGHT>
111.1

> <EXACT_MASS>
111.032028405

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
13

> <JCHEM_AVERAGE_POLARIZABILITY>
10.128236149349437

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
pyridine-2,5-diol

> <ALOGPS_LOGP>
-0.05

> <JCHEM_LOGP>
0.7429002756666667

> <ALOGPS_LOGS>
0.06

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.064063180277433

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.234971134796805

> <JCHEM_PKA_STRONGEST_BASIC>
2.2694474246180976

> <JCHEM_POLAR_SURFACE_AREA>
53.35000000000001

> <JCHEM_REFRACTIVITY>
28.176399999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.26e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2,5-dihydroxypyridine

> <JCHEM_VEBER_RULE>
0

$$$$

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3D-SDF for #<Metabolite:0x0000564322f8b810>
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PDB for #<Metabolite:0x0000564322f8b810>
HEADER    PROTEIN                                 04-JUN-15   NONE
TITLE     NULL                                                        
COMPND    MOLECULE:                                                   
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-JUN-15         0                                  
HETATM    1  C   UNK     0      22.891 -18.471   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      24.207 -19.248   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      22.891 -16.931   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0      21.568 -19.227   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0      25.544 -18.471   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0      24.207 -16.168   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0      25.544 -16.931   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      26.860 -16.168   0.000  0.00  0.00           O+0
CONECT    1    2    3    4                                                  
CONECT    2    1    5                                                       
CONECT    3    1    6                                                       
CONECT    4    1                                                            
CONECT    5    2    7                                                       
CONECT    6    3    7                                                       
CONECT    7    5    8    6                                                  
CONECT    8    7                                                            
MASTER        0    0    0    0    0    0    0    0    8    0   16    0
END

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3D PDB for #<Metabolite:0x0000564322f8b810>
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SMILES for #<Metabolite:0x0000564322f8b810>
OC1=CC=C(O)N=C1
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INCHI for #<Metabolite:0x0000564322f8b810>
InChI=1S/C5H5NO2/c7-4-1-2-5(8)6-3-4/h1-3,7H,(H,6,8)
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Synonyms
ValueSource
2,5-DihydroxypyridineChEBI
2,5-DHPYMeSH
Molecular FormulaC5H5NO2
Average Mass111.1
Monoisotopic Mass111.032028405
IUPAC Namepyridine-2,5-diol
Traditional Name2,5-dihydroxypyridine
CAS Registry NumberNot Available
SMILES
OC1=CC=C(O)N=C1
InChI Identifier
InChI=1S/C5H5NO2/c7-4-1-2-5(8)6-3-4/h1-3,7H,(H,6,8)
InChI KeyCHGPEDOMXOLANF-UHFFFAOYSA-N