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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2012-09-06 15:16:50 UTC

Update Date

2022-03-07 02:51:43 UTC

HMDB ID

HMDB0014739

Secondary Accession Numbers

HMDB14739

Metabolite Identification

Common Name

Linezolid

Description

Linezolid is only found in individuals that have used or taken this drug. It is a synthetic antibiotic, the first of the oxazolidinone class, used for the treatment of infections caused by multi-resistant bacteria including streptococcus and methicillin-resistant Staphylococcus aureus (MRSA). Linezolid is a synthetic antibacterial agent of the oxazolidinone class of antibiotics. It has in vitro activity against aerobic Gram positive bacteria, certain Gram negative bacteria and anaerobic microorganisms. It selectively inhibits bacterial protein synthesis through binding to sites on the bacterial ribosome and prevents the formation of a functional 70S-initiation complex. Specifically, linezolid binds to a site on the bacterial 23S ribosomal RNA of the 50S subunit and prevents the formation of a functional 70S initiation complex, which is an essential component of the bacterial translation process. The results of time-kill studies have shown linezolid to be bacteriostatic against enterococci and staphylococci. For streptococci, linezolid was found to be bactericidal for the majority of strains. Linezolid is also a reversible, nonselective inhibitor of monoamine oxidase. Therefore, linezolid has the potential for interaction with adrenergic and serotonergic agents.

Structure

MOL 3D MOL SDF 3D SDF PDB 3D PDB SMILES InChI

HMDB0014739
     RDKit          3D
Linezolid
 44 46  0  0  0  0  0  0  0  0999 V2000
    7.7611   -1.1141    1.3438 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4618   -0.4206    1.3043 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7750   -0.2829    2.3337 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.9899    0.0956    0.0737 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.7293    0.7700    0.0278 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5558   -0.0928    0.4605 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.3011    0.7141    0.2008 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3736   -0.1962   -0.4281 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0352   -0.0408   -0.4611 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8842   -0.9918   -0.9752 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2482   -0.8061   -0.9924 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8559    0.3455   -0.4952 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2598    0.4548   -0.5707 N   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0755   -0.6998   -1.0039 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4687   -0.4394   -0.4332 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4529    0.0628    0.8383 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8099    1.2662    1.0109 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0625    1.6157   -0.2775 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0117    1.2947    0.0186 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4847    2.4474    0.5383 F   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6470    1.1159    0.0387 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1663   -1.2317   -0.9805 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8202   -2.0227   -1.9335 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3718   -1.2325   -0.3081 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.9422   -1.4670    2.3775 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.7671   -2.0318    0.7129 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.6006   -0.4352    1.0562 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.5386    0.0015   -0.8180 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5787    1.1898   -0.9830 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7007    1.6620    0.7224 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5805   -0.2885    1.5536 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8496    1.0914    1.1199 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4764    1.5664   -0.4917 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4345   -1.9149   -1.3766 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8794   -1.5731   -1.4040 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6869   -1.6017   -0.4848 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1332   -0.7939   -2.0850 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0564    0.1567   -1.1487 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0018   -1.4356   -0.3653 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0312    1.0960    1.8125 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4674    2.0982    1.3289 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5496    2.5655   -0.2157 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8469    1.7700   -1.0883 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0427    1.8696    0.4469 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  2  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  2  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
 15 16  1  0
 16 17  1  0
 17 18  1  0
 12 19  1  0
 19 20  1  0
 19 21  2  0
  8 22  1  0
 22 23  2  0
 22 24  1  0
 24  6  1  0
 21  9  1  0
 18 13  1  0
  1 25  1  0
  1 26  1  0
  1 27  1  0
  4 28  1  0
  5 29  1  0
  5 30  1  0
  6 31  1  1
  7 32  1  0
  7 33  1  0
 10 34  1  0
 11 35  1  0
 14 36  1  0
 14 37  1  0
 15 38  1  0
 15 39  1  0
 17 40  1  0
 17 41  1  0
 18 42  1  0
 18 43  1  0
 21 44  1  0
M  END

601
  Mrv0541 02231214482D          

 24 26  0  0  1  0            999 V2000
    2.0883   -2.0559    0.0000 F   0  0  0  0  0  0  0  0  0  0  0  0
    3.9298    1.6887    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5173   -4.5309    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.9693    0.6491    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6500    3.6910    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5173    0.4191    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.5173   -2.8809    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.9554    3.1098    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.1048    1.6887    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.8498    0.9040    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2318   -3.2934    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8028   -3.2934    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5173   -0.4059    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6199    2.3561    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5173   -2.0559    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2318   -4.1184    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8028   -4.1184    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1848    0.9040    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8028   -0.8184    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2318   -0.8184    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8028   -1.6434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2318   -1.6434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4705    3.7772    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8061    4.5309    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1 21  1  0  0  0  0
  2  9  1  0  0  0  0
  2 18  1  0  0  0  0
  3 16  1  0  0  0  0
  3 17  1  0  0  0  0
  4 18  2  0  0  0  0
  5 23  2  0  0  0  0
  6 10  1  0  0  0  0
  6 13  1  0  0  0  0
  6 18  1  0  0  0  0
  7 11  1  0  0  0  0
  7 12  1  0  0  0  0
  7 15  1  0  0  0  0
  8 14  1  0  0  0  0
  8 23  1  0  0  0  0
  9 10  1  0  0  0  0
  9 14  1  6  0  0  0
 11 16  1  0  0  0  0
 12 17  1  0  0  0  0
 13 19  2  0  0  0  0
 13 20  1  0  0  0  0
 15 21  2  0  0  0  0
 15 22  1  0  0  0  0
 19 21  1  0  0  0  0
 20 22  2  0  0  0  0
 23 24  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0014739

> <DATABASE_NAME>
hmdb

> <SMILES>
CC(=O)NC[C@H]1CN(C(=O)O1)C1=CC(F)=C(C=C1)N1CCOCC1

> <INCHI_IDENTIFIER>
InChI=1S/C16H20FN3O4/c1-11(21)18-9-13-10-20(16(22)24-13)12-2-3-15(14(17)8-12)19-4-6-23-7-5-19/h2-3,8,13H,4-7,9-10H2,1H3,(H,18,21)/t13-/m0/s1

> <INCHI_KEY>
TYZROVQLWOKYKF-ZDUSSCGKSA-N

> <FORMULA>
C16H20FN3O4

> <MOLECULAR_WEIGHT>
337.3461

> <EXACT_MASS>
337.143784348

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_AVERAGE_POLARIZABILITY>
34.056244428194475

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
N-{[(5S)-3-[3-fluoro-4-(morpholin-4-yl)phenyl]-2-oxo-1,3-oxazolidin-5-yl]methyl}acetamide

> <ALOGPS_LOGP>
0.61

> <JCHEM_LOGP>
0.6366636523333332

> <ALOGPS_LOGS>
-2.37

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
14.453722188549907

> <JCHEM_PKA_STRONGEST_BASIC>
-0.6600890673965157

> <JCHEM_POLAR_SURFACE_AREA>
71.11

> <JCHEM_REFRACTIVITY>
84.47480000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.44e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
linezolid

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0014739
     RDKit          3D
Linezolid
 44 46  0  0  0  0  0  0  0  0999 V2000
    7.7611   -1.1141    1.3438 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4618   -0.4206    1.3043 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7750   -0.2829    2.3337 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.9899    0.0956    0.0737 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.7293    0.7700    0.0278 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5558   -0.0928    0.4605 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.3011    0.7141    0.2008 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3736   -0.1962   -0.4281 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0352   -0.0408   -0.4611 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8842   -0.9918   -0.9752 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2482   -0.8061   -0.9924 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8559    0.3455   -0.4952 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2598    0.4548   -0.5707 N   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0755   -0.6998   -1.0039 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4687   -0.4394   -0.4332 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4529    0.0628    0.8383 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8099    1.2662    1.0109 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0625    1.6157   -0.2775 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0117    1.2947    0.0186 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4847    2.4474    0.5383 F   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6470    1.1159    0.0387 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1663   -1.2317   -0.9805 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8202   -2.0227   -1.9335 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3718   -1.2325   -0.3081 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.9422   -1.4670    2.3775 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.7671   -2.0318    0.7129 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.6006   -0.4352    1.0562 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.5386    0.0015   -0.8180 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5787    1.1898   -0.9830 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7007    1.6620    0.7224 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5805   -0.2885    1.5536 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8496    1.0914    1.1199 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4764    1.5664   -0.4917 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4345   -1.9149   -1.3766 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8794   -1.5731   -1.4040 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6869   -1.6017   -0.4848 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1332   -0.7939   -2.0850 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0564    0.1567   -1.1487 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0018   -1.4356   -0.3653 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0312    1.0960    1.8125 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4674    2.0982    1.3289 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5496    2.5655   -0.2157 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8469    1.7700   -1.0883 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0427    1.8696    0.4469 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  2  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  2  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
 15 16  1  0
 16 17  1  0
 17 18  1  0
 12 19  1  0
 19 20  1  0
 19 21  2  0
  8 22  1  0
 22 23  2  0
 22 24  1  0
 24  6  1  0
 21  9  1  0
 18 13  1  0
  1 25  1  0
  1 26  1  0
  1 27  1  0
  4 28  1  0
  5 29  1  0
  5 30  1  0
  6 31  1  1
  7 32  1  0
  7 33  1  0
 10 34  1  0
 11 35  1  0
 14 36  1  0
 14 37  1  0
 15 38  1  0
 15 39  1  0
 17 40  1  0
 17 41  1  0
 18 42  1  0
 18 43  1  0
 21 44  1  0
M  END

HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: 601                                               
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  F   UNK     0       3.898  -3.838   0.000  0.00  0.00           F+0
HETATM    2  O   UNK     0       7.336   3.152   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0       6.566  -8.458   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0       9.276   1.212   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0       3.080   6.890   0.000  0.00  0.00           O+0
HETATM    6  N   UNK     0       6.566   0.782   0.000  0.00  0.00           N+0
HETATM    7  N   UNK     0       6.566  -5.378   0.000  0.00  0.00           N+0
HETATM    8  N   UNK     0       5.517   5.805   0.000  0.00  0.00           N+0
HETATM    9  C   UNK     0       5.796   3.152   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       5.320   1.687   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       7.899  -6.148   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       5.232  -6.148   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       6.566  -0.758   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       4.890   4.398   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       6.566  -3.838   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       7.899  -7.688   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       5.232  -7.688   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       7.812   1.687   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       5.232  -1.528   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       7.899  -1.528   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       5.232  -3.068   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       7.899  -3.068   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       4.612   7.051   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       5.238   8.458   0.000  0.00  0.00           C+0
CONECT    1   21                                                            
CONECT    2    9   18                                                       
CONECT    3   16   17                                                       
CONECT    4   18                                                            
CONECT    5   23                                                            
CONECT    6   10   13   18                                                  
CONECT    7   11   12   15                                                  
CONECT    8   14   23                                                       
CONECT    9    2   10   14                                                  
CONECT   10    6    9                                                       
CONECT   11    7   16                                                       
CONECT   12    7   17                                                       
CONECT   13    6   19   20                                                  
CONECT   14    8    9                                                       
CONECT   15    7   21   22                                                  
CONECT   16    3   11                                                       
CONECT   17    3   12                                                       
CONECT   18    2    4    6                                                  
CONECT   19   13   21                                                       
CONECT   20   13   22                                                       
CONECT   21    1   15   19                                                  
CONECT   22   15   20                                                       
CONECT   23    5    8   24                                                  
CONECT   24   23                                                            
MASTER        0    0    0    0    0    0    0    0   24    0   52    0
END

COMPND    HMDB0014739
HETATM    1  C1  UNL     1       7.761  -1.114   1.344  1.00  0.00           C  
HETATM    2  C2  UNL     1       6.462  -0.421   1.304  1.00  0.00           C  
HETATM    3  O1  UNL     1       5.775  -0.283   2.334  1.00  0.00           O  
HETATM    4  N1  UNL     1       5.990   0.096   0.074  1.00  0.00           N  
HETATM    5  C3  UNL     1       4.729   0.770   0.028  1.00  0.00           C  
HETATM    6  C4  UNL     1       3.556  -0.093   0.461  1.00  0.00           C  
HETATM    7  C5  UNL     1       2.301   0.714   0.201  1.00  0.00           C  
HETATM    8  N2  UNL     1       1.374  -0.196  -0.428  1.00  0.00           N  
HETATM    9  C6  UNL     1      -0.035  -0.041  -0.461  1.00  0.00           C  
HETATM   10  C7  UNL     1      -0.884  -0.992  -0.975  1.00  0.00           C  
HETATM   11  C8  UNL     1      -2.248  -0.806  -0.992  1.00  0.00           C  
HETATM   12  C9  UNL     1      -2.856   0.345  -0.495  1.00  0.00           C  
HETATM   13  N3  UNL     1      -4.260   0.455  -0.571  1.00  0.00           N  
HETATM   14  C10 UNL     1      -5.076  -0.700  -1.004  1.00  0.00           C  
HETATM   15  C11 UNL     1      -6.469  -0.439  -0.433  1.00  0.00           C  
HETATM   16  O2  UNL     1      -6.453   0.063   0.838  1.00  0.00           O  
HETATM   17  C12 UNL     1      -5.810   1.266   1.011  1.00  0.00           C  
HETATM   18  C13 UNL     1      -5.062   1.616  -0.278  1.00  0.00           C  
HETATM   19  C14 UNL     1      -2.012   1.295   0.019  1.00  0.00           C  
HETATM   20  F1  UNL     1      -2.485   2.447   0.538  1.00  0.00           F  
HETATM   21  C15 UNL     1      -0.647   1.116   0.039  1.00  0.00           C  
HETATM   22  C16 UNL     1       2.166  -1.232  -0.980  1.00  0.00           C  
HETATM   23  O3  UNL     1       1.820  -2.023  -1.933  1.00  0.00           O  
HETATM   24  O4  UNL     1       3.372  -1.233  -0.308  1.00  0.00           O  
HETATM   25  H1  UNL     1       7.942  -1.467   2.378  1.00  0.00           H  
HETATM   26  H2  UNL     1       7.767  -2.032   0.713  1.00  0.00           H  
HETATM   27  H3  UNL     1       8.601  -0.435   1.056  1.00  0.00           H  
HETATM   28  H4  UNL     1       6.539   0.001  -0.818  1.00  0.00           H  
HETATM   29  H5  UNL     1       4.579   1.190  -0.983  1.00  0.00           H  
HETATM   30  H6  UNL     1       4.701   1.662   0.722  1.00  0.00           H  
HETATM   31  H7  UNL     1       3.581  -0.289   1.554  1.00  0.00           H  
HETATM   32  H8  UNL     1       1.850   1.091   1.120  1.00  0.00           H  
HETATM   33  H9  UNL     1       2.476   1.566  -0.492  1.00  0.00           H  
HETATM   34  H10 UNL     1      -0.434  -1.915  -1.377  1.00  0.00           H  
HETATM   35  H11 UNL     1      -2.879  -1.573  -1.404  1.00  0.00           H  
HETATM   36  H12 UNL     1      -4.687  -1.602  -0.485  1.00  0.00           H  
HETATM   37  H13 UNL     1      -5.133  -0.794  -2.085  1.00  0.00           H  
HETATM   38  H14 UNL     1      -7.056   0.157  -1.149  1.00  0.00           H  
HETATM   39  H15 UNL     1      -7.002  -1.436  -0.365  1.00  0.00           H  
HETATM   40  H16 UNL     1      -5.031   1.096   1.813  1.00  0.00           H  
HETATM   41  H17 UNL     1      -6.467   2.098   1.329  1.00  0.00           H  
HETATM   42  H18 UNL     1      -4.550   2.565  -0.216  1.00  0.00           H  
HETATM   43  H19 UNL     1      -5.847   1.770  -1.088  1.00  0.00           H  
HETATM   44  H20 UNL     1       0.043   1.870   0.447  1.00  0.00           H  
CONECT    1    2   25   26   27
CONECT    2    3    3    4
CONECT    4    5   28
CONECT    5    6   29   30
CONECT    6    7   24   31
CONECT    7    8   32   33
CONECT    8    9   22
CONECT    9   10   10   21
CONECT   10   11   34
CONECT   11   12   12   35
CONECT   12   13   19
CONECT   13   14   18
CONECT   14   15   36   37
CONECT   15   16   38   39
CONECT   16   17
CONECT   17   18   40   41
CONECT   18   42   43
CONECT   19   20   21   21
CONECT   21   44
CONECT   22   23   23   24
END

HMDB0014739
     RDKit          3D
Linezolid
 44 46  0  0  0  0  0  0  0  0999 V2000
    7.7611   -1.1141    1.3438 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4618   -0.4206    1.3043 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7750   -0.2829    2.3337 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.9899    0.0956    0.0737 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.7293    0.7700    0.0278 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5558   -0.0928    0.4605 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.3011    0.7141    0.2008 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3736   -0.1962   -0.4281 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0352   -0.0408   -0.4611 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8842   -0.9918   -0.9752 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2482   -0.8061   -0.9924 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8559    0.3455   -0.4952 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2598    0.4548   -0.5707 N   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0755   -0.6998   -1.0039 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4687   -0.4394   -0.4332 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4529    0.0628    0.8383 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8099    1.2662    1.0109 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0625    1.6157   -0.2775 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0117    1.2947    0.0186 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4847    2.4474    0.5383 F   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6470    1.1159    0.0387 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1663   -1.2317   -0.9805 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8202   -2.0227   -1.9335 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3718   -1.2325   -0.3081 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.9422   -1.4670    2.3775 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.7671   -2.0318    0.7129 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.6006   -0.4352    1.0562 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.5386    0.0015   -0.8180 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5787    1.1898   -0.9830 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7007    1.6620    0.7224 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5805   -0.2885    1.5536 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8496    1.0914    1.1199 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4764    1.5664   -0.4917 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4345   -1.9149   -1.3766 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8794   -1.5731   -1.4040 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6869   -1.6017   -0.4848 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1332   -0.7939   -2.0850 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0564    0.1567   -1.1487 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0018   -1.4356   -0.3653 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0312    1.0960    1.8125 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4674    2.0982    1.3289 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5496    2.5655   -0.2157 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8469    1.7700   -1.0883 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0427    1.8696    0.4469 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  2  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  2  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
 15 16  1  0
 16 17  1  0
 17 18  1  0
 12 19  1  0
 19 20  1  0
 19 21  2  0
  8 22  1  0
 22 23  2  0
 22 24  1  0
 24  6  1  0
 21  9  1  0
 18 13  1  0
  1 25  1  0
  1 26  1  0
  1 27  1  0
  4 28  1  0
  5 29  1  0
  5 30  1  0
  6 31  1  1
  7 32  1  0
  7 33  1  0
 10 34  1  0
 11 35  1  0
 14 36  1  0
 14 37  1  0
 15 38  1  0
 15 39  1  0
 17 40  1  0
 17 41  1  0
 18 42  1  0
 18 43  1  0
 21 44  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Value	Source
N-(((S)-3-(3-Fluoro-4-morpholinophenyl)-2-oxo-5-oxazolidinyl)methyl)acetamide	ChEBI
Zyvox	Kegg
N-((3-(3-Fluoro-4-morpholinylphenyl)-2-oxo-5-oxazolidinyl)methyl)acetamide	HMDB
Linezolide	HMDB

Chemical Formula

C₁₆H₂₀FN₃O₄

Average Molecular Weight

337.3461

Monoisotopic Molecular Weight

337.143784348

IUPAC Name

N-{[(5S)-3-[3-fluoro-4-(morpholin-4-yl)phenyl]-2-oxo-1,3-oxazolidin-5-yl]methyl}acetamide

Traditional Name

linezolid

CAS Registry Number

165800-03-3

SMILES

CC(=O)NC[C@H]1CN(C(=O)O1)C1=CC(F)=C(C=C1)N1CCOCC1

InChI Identifier

InChI=1S/C16H20FN3O4/c1-11(21)18-9-13-10-20(16(22)24-13)12-2-3-15(14(17)8-12)19-4-6-23-7-5-19/h2-3,8,13H,4-7,9-10H2,1H3,(H,18,21)/t13-/m0/s1

InChI Key

TYZROVQLWOKYKF-ZDUSSCGKSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as phenylmorpholines. These are aromatic compounds containing a morpholine ring and a benzene ring linked to each other through a CC or a CN bond.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Oxazinanes

Sub Class

Morpholines

Direct Parent

Phenylmorpholines

Alternative Parents

Substituents

Phenylmorpholine
Aniline or substituted anilines
Tertiary aliphatic/aromatic amine
Dialkylarylamine
Fluorobenzene
Halobenzene
Aryl fluoride
Aryl halide
Monocyclic benzene moiety
Oxazolidinone
Benzenoid
Oxazolidine
Acetamide
Carbamic acid ester
Secondary carboxylic acid amide
Tertiary amine
Amino acid or derivatives
Carboxamide group
Carbonic acid derivative
Azacycle
Oxacycle
Carboxylic acid derivative
Dialkyl ether
Ether
Amine
Organic oxide
Hydrocarbon derivative
Organohalogen compound
Organofluoride
Organonitrogen compound
Carbonyl group
Organopnictogen compound
Organic oxygen compound
Organic nitrogen compound
Organooxygen compound
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

organofluorine compound (CHEBI:63607 )
acetamides (CHEBI:63607 )
morpholines (CHEBI:63607 )
oxazolidinone (CHEBI:63607 )

Ontology

Physiological effect

Not Available

Disposition

Biological location

Non-excretory biofluid

Biofluid or Excreta

Blood (PMID: 21059682)

Excreta

Biofluid or Excreta

Urine (PMID: 21059682)

Cellular substructure

Cytoplasm (HMDB: HMDB0014739)
Extracellular (HMDB: HMDB0014739)

Cell

Nerve cell (HMDB: HMDB0014739)

Tissue

Connective tissue

Bone marrow (HMDB: HMDB0014739)

Organ

Eye (HMDB: HMDB0014739)

Source

Exogenous

Exogenous (HMDB: HMDB0014739)

Process

Not Available

Role

Industrial application

Pharmaceutical industry

Antibacterial drug (HMDB: HMDB0014739)

Protein synthesis inhibitor (HMDB: HMDB0014739)

Physical Properties

State

Solid

Experimental Molecular Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	1.44 g/L	Not Available
LogP	0.9	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
Water Solubility	1.44 g/L	ALOGPS
logP	0.61	ALOGPS
logP	0.64	ChemAxon
logS	-2.4	ALOGPS
pKa (Strongest Acidic)	14.45	ChemAxon
pKa (Strongest Basic)	-0.66	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	71.11 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	84.47 m³·mol⁻¹	ChemAxon
Polarizability	34.06 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DeepCCS	[M+H]+	173.441	30932474
DeepCCS	[M-H]-	171.041	30932474
DeepCCS	[M-2H]-	205.375	30932474
DeepCCS	[M+Na]+	180.594	30932474
AllCCS	[M+H]+	177.0	32859911
AllCCS	[M+H-H2O]+	174.1	32859911
AllCCS	[M+NH4]+	179.7	32859911
AllCCS	[M+Na]+	180.4	32859911
AllCCS	[M-H]-	178.0	32859911
AllCCS	[M+Na-2H]-	177.9	32859911
AllCCS	[M+HCOO]-	178.0	32859911

Predicted Retention Times

Underivatized

Chromatographic Method	Retention Time	Reference
Measured using a Waters Acquity ultraperformance liquid chromatography (UPLC) ethylene-bridged hybrid (BEH) C18 column (100 mm × 2.1 mm; 1.7 μmparticle diameter). Predicted by Afia on May 17, 2022. Predicted by Afia on May 17, 2022.	3.76 minutes	32390414
Predicted by Siyang on May 30, 2022	11.5234 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	1.68 minutes	32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	1663.0 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	225.7 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	145.5 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	169.3 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	62.4 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	342.4 seconds	40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid	440.7 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	72.7 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	913.5 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	354.1 seconds	40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid	1317.8 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	299.2 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	315.3 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	338.9 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	136.5 seconds	40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water	20.1 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Linezolid	CC(=O)NC[C@H]1CN(C(=O)O1)C1=CC(F)=C(C=C1)N1CCOCC1	3525.9	Standard polar	33892256
Linezolid	CC(=O)NC[C@H]1CN(C(=O)O1)C1=CC(F)=C(C=C1)N1CCOCC1	2876.9	Standard non polar	33892256
Linezolid	CC(=O)NC[C@H]1CN(C(=O)O1)C1=CC(F)=C(C=C1)N1CCOCC1	3237.8	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Linezolid,1TMS,isomer #1	CC(=O)N(C[C@H]1CN(C2=CC=C(N3CCOCC3)C(F)=C2)C(=O)O1)[Si](C)(C)C	2895.6	Semi standard non polar	33892256
Linezolid,1TMS,isomer #1	CC(=O)N(C[C@H]1CN(C2=CC=C(N3CCOCC3)C(F)=C2)C(=O)O1)[Si](C)(C)C	2681.9	Standard non polar	33892256
Linezolid,1TMS,isomer #1	CC(=O)N(C[C@H]1CN(C2=CC=C(N3CCOCC3)C(F)=C2)C(=O)O1)[Si](C)(C)C	3772.9	Standard polar	33892256
Linezolid,1TBDMS,isomer #1	CC(=O)N(C[C@H]1CN(C2=CC=C(N3CCOCC3)C(F)=C2)C(=O)O1)[Si](C)(C)C(C)(C)C	3100.3	Semi standard non polar	33892256
Linezolid,1TBDMS,isomer #1	CC(=O)N(C[C@H]1CN(C2=CC=C(N3CCOCC3)C(F)=C2)C(=O)O1)[Si](C)(C)C(C)(C)C	2941.0	Standard non polar	33892256
Linezolid,1TBDMS,isomer #1	CC(=O)N(C[C@H]1CN(C2=CC=C(N3CCOCC3)C(F)=C2)C(=O)O1)[Si](C)(C)C(C)(C)C	3835.4	Standard polar	33892256

Spectra

Biological Properties

Cellular Locations

Cytoplasm

Biospecimen Locations

Blood
Urine

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Expected but not Quantified	Not Quantified	Not Available	Not Available	Taking drug identified by DrugBank entry DB00601	21059682	details
Urine	Expected but not Quantified	Not Quantified	Not Available	Not Available	Taking drug identified by DrugBank entry DB00601	21059682	details

Abnormal Concentrations

Not Available

Predicted Concentrations

Biospecimen	Value	Original age	Original sex	Original condition	Comments
Blood	0.000 uM	Adult (>18 years old)	Both	Normal	Predicted based on drug qualities
Blood	0.000 umol/mmol creatinine	Adult (>18 years old)	Both	Normal	Predicted based on drug qualities

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

DB00601

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

390139

KEGG Compound ID

C08146

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Linezolid

METLIN ID

Not Available

PubChem Compound

441401

PDB ID

ZLD

ChEBI ID

63607

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

Park IN, Hong SB, Oh YM, Kim MN, Lim CM, Lee SD, Koh Y, Kim WS, Kim DS, Kim WD, Shim TS: Efficacy and tolerability of daily-half dose linezolid in patients with intractable multidrug-resistant tuberculosis. J Antimicrob Chemother. 2006 Sep;58(3):701-4. Epub 2006 Jul 19. [PubMed:16857689 ]
South African Electronic Package Inserts [Link]

Enzymes

Enzyme Details

1. Amine oxidase [flavin-containing] B

General function:: Involved in oxidoreductase activity
Specific function:: Catalyzes the oxidative deamination of biogenic and xenobiotic amines and has important functions in the metabolism of neuroactive and vasoactive amines in the central nervous system and peripheral tissues. MAOB preferentially degrades benzylamine and phenylethylamine.
Gene Name:: MAOB
Uniprot ID:: P27338
Molecular weight:: 58762.475

References

Stevens DL, Dotter B, Madaras-Kelly K: A review of linezolid: the first oxazolidinone antibiotic. Expert Rev Anti Infect Ther. 2004 Feb;2(1):51-9. [PubMed:15482171 ]
Taylor JJ, Wilson JW, Estes LL: Linezolid and serotonergic drug interactions: a retrospective survey. Clin Infect Dis. 2006 Jul 15;43(2):180-7. Epub 2006 Jun 9. [PubMed:16779744 ]

Enzyme Details

2. Amine oxidase [flavin-containing] A

General function:: Involved in oxidoreductase activity
Specific function:: Catalyzes the oxidative deamination of biogenic and xenobiotic amines and has important functions in the metabolism of neuroactive and vasoactive amines in the central nervous system and peripheral tissues. MAOA preferentially oxidizes biogenic amines such as 5-hydroxytryptamine (5-HT), norepinephrine and epinephrine.
Gene Name:: MAOA
Uniprot ID:: P21397
Molecular weight:: 59681.27

References

Stevens DL, Dotter B, Madaras-Kelly K: A review of linezolid: the first oxazolidinone antibiotic. Expert Rev Anti Infect Ther. 2004 Feb;2(1):51-9. [PubMed:15482171 ]
Taylor JJ, Wilson JW, Estes LL: Linezolid and serotonergic drug interactions: a retrospective survey. Clin Infect Dis. 2006 Jul 15;43(2):180-7. Epub 2006 Jun 9. [PubMed:16779744 ]

Showing metabocard for Linezolid (HMDB0014739)

MOL for HMDB0014739 (Linezolid)

3D MOL for HMDB0014739 (Linezolid)

3D SDF for HMDB0014739 (Linezolid)

3D-SDF for HMDB0014739 (Linezolid)

PDB for HMDB0014739 (Linezolid)

3D PDB for HMDB0014739 (Linezolid)

SMILES for HMDB0014739 (Linezolid)

INCHI for HMDB0014739 (Linezolid)

Structure for HMDB0014739 (Linezolid)

3D Structure for HMDB0014739 (Linezolid)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

Derivatized

Enzymes

References

References