Hmdb loader

Showing metabocard for Nitrogenase (HMDB0302648)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2021-09-23 19:24:08 UTC
Update Date2021-09-23 19:24:08 UTC
HMDB IDHMDB0302648
Secondary Accession NumbersNone
Metabolite Identification
Common NameNitrogenase
Description Nitrogenase can be found in soy bean, which makes nitrogenase a potential biomarker for the consumption of this food product. Nitrogenases are enzymes (EC 1.18.6.1EC 1.19.6.1) that are produced by certain bacteria, such as cyanobacteria (blue-green algae). These enzymes are responsible for the reduction of nitrogen (N2) to ammonia (NH3). Nitrogenases are the only family of enzymes known to catalyze this reaction, which is a key step in the process of nitrogen fixation. Nitrogen fixation is required for all forms of life, with nitrogen being essential for the biosynthesis of molecules (nucleotides, amino acids) that create plants, animals and other organisms .
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0302648 (Nitrogenase)

  Mrv0541 02241220492D          

 32 13  0  0  0  0            999 V2000
    1.0444   -0.2955    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4724    0.2990    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3285    0.1008    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1293   -0.0973    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7014    0.4972    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5022    0.2990    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4725    1.2898    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -0.1303   -0.7000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7248   -1.2720    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6623   -0.9288    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5266    0.9017    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8453   -0.0973    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0741    0.6953    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4173   -0.6918    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    4.7744    0.0000    0.0000 N   0  5  0  0  0  0  0  0  0  0  0  0
    5.7762    0.0000    0.0000 S   0  5  0  0  0  0  0  0  0  0  0  0
    6.7780    0.0000    0.0000 S   0  5  0  0  0  0  0  0  0  0  0  0
    0.0000   -2.9220    0.0000 S   0  5  0  0  0  0  0  0  0  0  0  0
    1.0018   -2.9220    0.0000 S   0  5  0  0  0  0  0  0  0  0  0  0
    2.0036   -2.9220    0.0000 S   0  5  0  0  0  0  0  0  0  0  0  0
    3.0054   -2.9220    0.0000 S   0  5  0  0  0  0  0  0  0  0  0  0
    0.0000   -4.5720    0.0000 S   0  5  0  0  0  0  0  0  0  0  0  0
    1.0018   -4.5720    0.0000 S   0  5  0  0  0  0  0  0  0  0  0  0
    2.0036   -4.5720    0.0000 S   0  5  0  0  0  0  0  0  0  0  0  0
    4.1250   -4.5720    0.0000 Fe  0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -6.2220    0.0000 Fe  0  0  0  0  0  0  0  0  0  0  0  0
    2.1214   -6.2220    0.0000 Fe  0  0  0  0  0  0  0  0  0  0  0  0
    4.2429   -6.2220    0.0000 Fe  0  0  0  0  0  0  0  0  0  0  0  0
    6.3643   -6.2220    0.0000 Fe  0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -7.8720    0.0000 Fe  0  0  0  0  0  0  0  0  0  0  0  0
    2.1214   -7.8720    0.0000 Fe  0  0  0  0  0  0  0  0  0  0  0  0
    4.2429   -7.8720    0.0000 Mo  0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  5  7  1  0  0  0  0
  3  8  1  0  0  0  0
  8  9  2  0  0  0  0
  8 10  1  0  0  0  0
  3 11  1  0  0  0  0
  1 12  1  0  0  0  0
 12 13  2  0  0  0  0
 12 14  1  0  0  0  0
M  CHG  8   7  -1  14  -1  15  -1  16  -1  17  -1  18  -1  19  -1  20  -1
M  CHG  4  21  -1  22  -1  23  -1  24  -1
M  END
Download

3D MOL for HMDB0302648 (Nitrogenase)

HMDB0302648
     RDKit          3D
Nitrogenase
 51 32  0  0  0  0  0  0  0  0999 V2000
    3.2723    0.9836   -0.2103 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0438   -0.2393   -0.1195 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0553   -1.1582   -0.2765 O   0  0  0  0  0  1  0  0  0  0  0  0
    1.6757   -0.7017    0.1587 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7147    0.4660    0.2965 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6535   -0.0955    0.5784 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5039   -0.8236    1.7923 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6840    0.9337    0.8726 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9423    1.9250   -0.1618 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3355    1.9438   -1.2334 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9130    2.8877    0.0708 O   0  0  0  0  0  1  0  0  0  0  0  0
   -1.0228   -1.0394   -0.4848 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1989   -0.6253   -1.6535 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1763   -2.3724   -0.2059 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 Fe  0  0  0  0  0 15  0  0  0  0  0  0
    0.0000    0.0000    0.0000 Fe  0  0  0  0  0 15  0  0  0  0  0  0
    0.0000    0.0000    0.0000 Fe  0  0  0  0  0 15  0  0  0  0  0  0
    0.0000    0.0000    0.0000 Fe  0  0  0  0  0 15  0  0  0  0  0  0
    0.0000    0.0000    0.0000 Fe  0  0  0  0  0 15  0  0  0  0  0  0
    0.0000    0.0000    0.0000 Fe  0  0  0  0  0 15  0  0  0  0  0  0
    0.0000    0.0000    0.0000 Fe  0  0  0  0  0 15  0  0  0  0  0  0
    0.0000    0.0000    0.0000 Mo  0  0  0  0  0 15  0  0  0  0  0  0
   -0.0026    0.3960   -0.0000 N   0  0  0  0  0  2  0  0  0  0  0  0
    0.6857    0.0000    0.0000 S   0  0  0  0  0  1  0  0  0  0  0  0
    0.6830    0.0000    0.0000 S   0  0  0  0  0  1  0  0  0  0  0  0
    0.6830    0.0000    0.0000 S   0  0  0  0  0  1  0  0  0  0  0  0
    0.6811    0.0000    0.0000 S   0  0  0  0  0  1  0  0  0  0  0  0
    0.6850    0.0000    0.0000 S   0  0  0  0  0  1  0  0  0  0  0  0
    0.6843    0.0000    0.0000 S   0  0  0  0  0  1  0  0  0  0  0  0
    0.6826    0.0000    0.0000 S   0  0  0  0  0  1  0  0  0  0  0  0
    0.6876    0.0000    0.0000 S   0  0  0  0  0  1  0  0  0  0  0  0
    0.6876    0.0000    0.0000 S   0  0  0  0  0  1  0  0  0  0  0  0
    1.3372   -1.4227   -0.6125 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7255   -1.2953    1.1130 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0850    1.1194    1.1022 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7536    1.0377   -0.6423 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0933   -0.1805    2.4225 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6475    0.3714    1.0577 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4815    1.4257    1.8637 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0106   -3.1400   -0.8421 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8671   -0.1971    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8646   -0.1989   -0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6857    0.0000    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6830    0.0000    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6830    0.0000    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6811    0.0000    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6850    0.0000    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6843    0.0000    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6826    0.0000    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6876    0.0000    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6876    0.0000    0.0000 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  1  0
  6  7  1  0
  6  8  1  0
  8  9  1  0
  9 10  2  0
  9 11  1  0
  6 12  1  0
 12 13  2  0
 12 14  1  0
  4 33  1  0
  4 34  1  0
  5 35  1  0
  5 36  1  0
  7 37  1  0
  8 38  1  0
  8 39  1  0
 14 40  1  0
 23 41  1  0
 23 42  1  0
 24 43  1  0
 25 44  1  0
 26 45  1  0
 27 46  1  0
 28 47  1  0
 29 48  1  0
 30 49  1  0
 31 50  1  0
 32 51  1  0
M  CHG  8   3  -1  11  -1  23  -1  24  -1  25  -1  26  -1  27  -1  28  -1
M  CHG  4  29  -1  30  -1  31  -1  32  -1
M  END
Download

3D SDF for HMDB0302648 (Nitrogenase)

  Mrv0541 02241220492D          

 32 13  0  0  0  0            999 V2000
    1.0444   -0.2955    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4724    0.2990    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3285    0.1008    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1293   -0.0973    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7014    0.4972    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5022    0.2990    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4725    1.2898    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -0.1303   -0.7000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7248   -1.2720    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6623   -0.9288    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5266    0.9017    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8453   -0.0973    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0741    0.6953    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4173   -0.6918    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    4.7744    0.0000    0.0000 N   0  5  0  0  0  0  0  0  0  0  0  0
    5.7762    0.0000    0.0000 S   0  5  0  0  0  0  0  0  0  0  0  0
    6.7780    0.0000    0.0000 S   0  5  0  0  0  0  0  0  0  0  0  0
    0.0000   -2.9220    0.0000 S   0  5  0  0  0  0  0  0  0  0  0  0
    1.0018   -2.9220    0.0000 S   0  5  0  0  0  0  0  0  0  0  0  0
    2.0036   -2.9220    0.0000 S   0  5  0  0  0  0  0  0  0  0  0  0
    3.0054   -2.9220    0.0000 S   0  5  0  0  0  0  0  0  0  0  0  0
    0.0000   -4.5720    0.0000 S   0  5  0  0  0  0  0  0  0  0  0  0
    1.0018   -4.5720    0.0000 S   0  5  0  0  0  0  0  0  0  0  0  0
    2.0036   -4.5720    0.0000 S   0  5  0  0  0  0  0  0  0  0  0  0
    4.1250   -4.5720    0.0000 Fe  0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -6.2220    0.0000 Fe  0  0  0  0  0  0  0  0  0  0  0  0
    2.1214   -6.2220    0.0000 Fe  0  0  0  0  0  0  0  0  0  0  0  0
    4.2429   -6.2220    0.0000 Fe  0  0  0  0  0  0  0  0  0  0  0  0
    6.3643   -6.2220    0.0000 Fe  0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -7.8720    0.0000 Fe  0  0  0  0  0  0  0  0  0  0  0  0
    2.1214   -7.8720    0.0000 Fe  0  0  0  0  0  0  0  0  0  0  0  0
    4.2429   -7.8720    0.0000 Mo  0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  5  7  1  0  0  0  0
  3  8  1  0  0  0  0
  8  9  2  0  0  0  0
  8 10  1  0  0  0  0
  3 11  1  0  0  0  0
  1 12  1  0  0  0  0
 12 13  2  0  0  0  0
 12 14  1  0  0  0  0
M  CHG  8   7  -1  14  -1  15  -1  16  -1  17  -1  18  -1  19  -1  20  -1
M  CHG  4  21  -1  22  -1  23  -1  24  -1
M  END
> <DATABASE_ID>
HMDB0302648

> <DATABASE_NAME>
hmdb

> <SMILES>
[NH2-].[SH-].[SH-].[SH-].[SH-].[SH-].[SH-].[SH-].[SH-].[SH-].[Fe].[Fe].[Fe].[Fe].[Fe].[Fe].[Fe].[Mo].OC(=O)C(O)(CCC([O-])=O)CC([O-])=O

> <INCHI_IDENTIFIER>
InChI=1S/C7H10O7.7Fe.Mo.H2N.9H2S/c8-4(9)1-2-7(14,6(12)13)3-5(10)11;;;;;;;;;;;;;;;;;;/h14H,1-3H2,(H,8,9)(H,10,11)(H,12,13);;;;;;;;;10*1H2/q;;;;;;;;;-1;;;;;;;;;/p-11

> <INCHI_KEY>
OUNCJAISYHCMSR-UHFFFAOYSA-C

> <FORMULA>
C7H19Fe7MoNO7S9

> <MOLECULAR_WEIGHT>
1004.67

> <EXACT_MASS>
1006.314790954

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_AVERAGE_POLARIZABILITY>
16.721701578354047

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
-12

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3-carboxy-3-hydroxyhexanedioate heptairon molybdenum azanide nonasulfanide

> <JCHEM_LOGP>
-1.0340262470000003

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-3

> <JCHEM_PKA>
3.9251914717112886

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.0867039911638208

> <JCHEM_PKA_STRONGEST_BASIC>
-4.0751445556736625

> <JCHEM_POLAR_SURFACE_AREA>
137.79

> <JCHEM_REFRACTIVITY>
62.05310000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
3-hydroxy-3-carboxyadipate heptairon molybdenum azanide nonasulfanide

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0302648 (Nitrogenase)

HMDB0302648
     RDKit          3D
Nitrogenase
 51 32  0  0  0  0  0  0  0  0999 V2000
    3.2723    0.9836   -0.2103 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0438   -0.2393   -0.1195 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0553   -1.1582   -0.2765 O   0  0  0  0  0  1  0  0  0  0  0  0
    1.6757   -0.7017    0.1587 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7147    0.4660    0.2965 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6535   -0.0955    0.5784 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5039   -0.8236    1.7923 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6840    0.9337    0.8726 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9423    1.9250   -0.1618 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3355    1.9438   -1.2334 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9130    2.8877    0.0708 O   0  0  0  0  0  1  0  0  0  0  0  0
   -1.0228   -1.0394   -0.4848 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1989   -0.6253   -1.6535 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1763   -2.3724   -0.2059 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 Fe  0  0  0  0  0 15  0  0  0  0  0  0
    0.0000    0.0000    0.0000 Fe  0  0  0  0  0 15  0  0  0  0  0  0
    0.0000    0.0000    0.0000 Fe  0  0  0  0  0 15  0  0  0  0  0  0
    0.0000    0.0000    0.0000 Fe  0  0  0  0  0 15  0  0  0  0  0  0
    0.0000    0.0000    0.0000 Fe  0  0  0  0  0 15  0  0  0  0  0  0
    0.0000    0.0000    0.0000 Fe  0  0  0  0  0 15  0  0  0  0  0  0
    0.0000    0.0000    0.0000 Fe  0  0  0  0  0 15  0  0  0  0  0  0
    0.0000    0.0000    0.0000 Mo  0  0  0  0  0 15  0  0  0  0  0  0
   -0.0026    0.3960   -0.0000 N   0  0  0  0  0  2  0  0  0  0  0  0
    0.6857    0.0000    0.0000 S   0  0  0  0  0  1  0  0  0  0  0  0
    0.6830    0.0000    0.0000 S   0  0  0  0  0  1  0  0  0  0  0  0
    0.6830    0.0000    0.0000 S   0  0  0  0  0  1  0  0  0  0  0  0
    0.6811    0.0000    0.0000 S   0  0  0  0  0  1  0  0  0  0  0  0
    0.6850    0.0000    0.0000 S   0  0  0  0  0  1  0  0  0  0  0  0
    0.6843    0.0000    0.0000 S   0  0  0  0  0  1  0  0  0  0  0  0
    0.6826    0.0000    0.0000 S   0  0  0  0  0  1  0  0  0  0  0  0
    0.6876    0.0000    0.0000 S   0  0  0  0  0  1  0  0  0  0  0  0
    0.6876    0.0000    0.0000 S   0  0  0  0  0  1  0  0  0  0  0  0
    1.3372   -1.4227   -0.6125 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7255   -1.2953    1.1130 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0850    1.1194    1.1022 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7536    1.0377   -0.6423 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0933   -0.1805    2.4225 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6475    0.3714    1.0577 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4815    1.4257    1.8637 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0106   -3.1400   -0.8421 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8671   -0.1971    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8646   -0.1989   -0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6857    0.0000    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6830    0.0000    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6830    0.0000    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6811    0.0000    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6850    0.0000    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6843    0.0000    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6826    0.0000    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6876    0.0000    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6876    0.0000    0.0000 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  1  0
  6  7  1  0
  6  8  1  0
  8  9  1  0
  9 10  2  0
  9 11  1  0
  6 12  1  0
 12 13  2  0
 12 14  1  0
  4 33  1  0
  4 34  1  0
  5 35  1  0
  5 36  1  0
  7 37  1  0
  8 38  1  0
  8 39  1  0
 14 40  1  0
 23 41  1  0
 23 42  1  0
 24 43  1  0
 25 44  1  0
 26 45  1  0
 27 46  1  0
 28 47  1  0
 29 48  1  0
 30 49  1  0
 31 50  1  0
 32 51  1  0
M  CHG  8   3  -1  11  -1  23  -1  24  -1  25  -1  26  -1  27  -1  28  -1
M  CHG  4  29  -1  30  -1  31  -1  32  -1
M  END
Download

PDB for HMDB0302648 (Nitrogenase)

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       1.950  -0.552   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.882   0.558   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -0.613   0.188   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -2.108  -0.182   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -3.176   0.928   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      -4.671   0.558   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0      -2.749   2.408   0.000  0.00  0.00           O-1
HETATM    8  C   UNK     0      -0.243  -1.307   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0      -1.353  -2.374   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0       1.236  -1.734   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0      -0.983   1.683   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0       3.445  -0.182   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       3.872   1.298   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0       4.512  -1.291   0.000  0.00  0.00           O-1
HETATM   15  N   UNK     0       8.912   0.000   0.000  0.00  0.00           N-1
HETATM   16  S   UNK     0      10.782   0.000   0.000  0.00  0.00           S-1
HETATM   17  S   UNK     0      12.652   0.000   0.000  0.00  0.00           S-1
HETATM   18  S   UNK     0       0.000  -5.454   0.000  0.00  0.00           S-1
HETATM   19  S   UNK     0       1.870  -5.454   0.000  0.00  0.00           S-1
HETATM   20  S   UNK     0       3.740  -5.454   0.000  0.00  0.00           S-1
HETATM   21  S   UNK     0       5.610  -5.454   0.000  0.00  0.00           S-1
HETATM   22  S   UNK     0       0.000  -8.534   0.000  0.00  0.00           S-1
HETATM   23  S   UNK     0       1.870  -8.534   0.000  0.00  0.00           S-1
HETATM   24  S   UNK     0       3.740  -8.534   0.000  0.00  0.00           S-1
HETATM   25 Fe   UNK     0       7.700  -8.534   0.000  0.00  0.00          Fe+0
HETATM   26 Fe   UNK     0       0.000 -11.614   0.000  0.00  0.00          Fe+0
HETATM   27 Fe   UNK     0       3.960 -11.614   0.000  0.00  0.00          Fe+0
HETATM   28 Fe   UNK     0       7.920 -11.614   0.000  0.00  0.00          Fe+0
HETATM   29 Fe   UNK     0      11.880 -11.614   0.000  0.00  0.00          Fe+0
HETATM   30 Fe   UNK     0       0.000 -14.694   0.000  0.00  0.00          Fe+0
HETATM   31 Fe   UNK     0       3.960 -14.694   0.000  0.00  0.00          Fe+0
HETATM   32 Mo   UNK     0       7.920 -14.694   0.000  0.00  0.00          Mo+0
CONECT    1    2   12                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4    8   11                                             
CONECT    4    3    5                                                       
CONECT    5    4    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5                                                            
CONECT    8    3    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8                                                            
CONECT   11    3                                                            
CONECT   12    1   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12                                                            
MASTER        0    0    0    0    0    0    0    0   32    0   26    0
END
Download

3D PDB for HMDB0302648 (Nitrogenase)

COMPND    HMDB0302648
HETATM    1  O1  UNL     1       3.272   0.984  -0.210  1.00  0.00           O  
HETATM    2  C1  UNL     1       3.044  -0.239  -0.120  1.00  0.00           C  
HETATM    3  O2  UNL     1       4.055  -1.158  -0.276  1.00  0.00           O1-
HETATM    4  C2  UNL     1       1.676  -0.702   0.159  1.00  0.00           C  
HETATM    5  C3  UNL     1       0.715   0.466   0.296  1.00  0.00           C  
HETATM    6  C4  UNL     1      -0.654  -0.095   0.578  1.00  0.00           C  
HETATM    7  O3  UNL     1      -0.504  -0.824   1.792  1.00  0.00           O  
HETATM    8  C5  UNL     1      -1.684   0.934   0.873  1.00  0.00           C  
HETATM    9  C6  UNL     1      -1.942   1.925  -0.162  1.00  0.00           C  
HETATM   10  O4  UNL     1      -1.335   1.944  -1.233  1.00  0.00           O  
HETATM   11  O5  UNL     1      -2.913   2.888   0.071  1.00  0.00           O1-
HETATM   12  C7  UNL     1      -1.023  -1.039  -0.485  1.00  0.00           C  
HETATM   13  O6  UNL     1      -1.199  -0.625  -1.654  1.00  0.00           O  
HETATM   14  O7  UNL     1      -1.176  -2.372  -0.206  1.00  0.00           O  
HETATM   15 FE1  UNL     1       0.000   0.000   0.000  1.00  0.00          FE  
HETATM   16 FE2  UNL     1       0.000   0.000   0.000  1.00  0.00          FE  
HETATM   17 FE3  UNL     1       0.000   0.000   0.000  1.00  0.00          FE  
HETATM   18 FE4  UNL     1       0.000   0.000   0.000  1.00  0.00          FE  
HETATM   19 FE5  UNL     1       0.000   0.000   0.000  1.00  0.00          FE  
HETATM   20 FE6  UNL     1       0.000   0.000   0.000  1.00  0.00          FE  
HETATM   21 FE7  UNL     1       0.000   0.000   0.000  1.00  0.00          FE  
HETATM   22 MO1  UNL     1       0.000   0.000   0.000  1.00  0.00          MO  
HETATM   23  N1  UNL     1      -0.003   0.396  -0.000  1.00  0.00           N1-
HETATM   24  S1  UNL     1       0.686   0.000   0.000  1.00  0.00           S1-
HETATM   25  S2  UNL     1       0.683   0.000   0.000  1.00  0.00           S1-
HETATM   26  S3  UNL     1       0.683   0.000   0.000  1.00  0.00           S1-
HETATM   27  S4  UNL     1       0.681   0.000   0.000  1.00  0.00           S1-
HETATM   28  S5  UNL     1       0.685   0.000   0.000  1.00  0.00           S1-
HETATM   29  S6  UNL     1       0.684   0.000   0.000  1.00  0.00           S1-
HETATM   30  S7  UNL     1       0.683   0.000   0.000  1.00  0.00           S1-
HETATM   31  S8  UNL     1       0.688   0.000   0.000  1.00  0.00           S1-
HETATM   32  S9  UNL     1       0.688   0.000   0.000  1.00  0.00           S1-
HETATM   33  H1  UNL     1       1.337  -1.423  -0.612  1.00  0.00           H  
HETATM   34  H2  UNL     1       1.725  -1.295   1.113  1.00  0.00           H  
HETATM   35  H3  UNL     1       1.085   1.119   1.102  1.00  0.00           H  
HETATM   36  H4  UNL     1       0.754   1.038  -0.642  1.00  0.00           H  
HETATM   37  H5  UNL     1      -0.093  -0.181   2.422  1.00  0.00           H  
HETATM   38  H6  UNL     1      -2.647   0.371   1.058  1.00  0.00           H  
HETATM   39  H7  UNL     1      -1.481   1.426   1.864  1.00  0.00           H  
HETATM   40  H8  UNL     1      -1.011  -3.140  -0.842  1.00  0.00           H  
HETATM   41  H9  UNL     1       0.867  -0.197   0.000  1.00  0.00           H  
HETATM   42  H10 UNL     1      -0.865  -0.199  -0.000  1.00  0.00           H  
HETATM   43  H11 UNL     1      -0.686   0.000   0.000  1.00  0.00           H  
HETATM   44  H12 UNL     1      -0.683   0.000   0.000  1.00  0.00           H  
HETATM   45  H13 UNL     1      -0.683   0.000   0.000  1.00  0.00           H  
HETATM   46  H14 UNL     1      -0.681   0.000   0.000  1.00  0.00           H  
HETATM   47  H15 UNL     1      -0.685   0.000   0.000  1.00  0.00           H  
HETATM   48  H16 UNL     1      -0.684   0.000   0.000  1.00  0.00           H  
HETATM   49  H17 UNL     1      -0.683   0.000   0.000  1.00  0.00           H  
HETATM   50  H18 UNL     1      -0.688   0.000   0.000  1.00  0.00           H  
HETATM   51  H19 UNL     1      -0.688   0.000   0.000  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    4
CONECT    4    5   33   34
CONECT    5    6   35   36
CONECT    6    7    8   12
CONECT    7   37
CONECT    8    9   38   39
CONECT    9   10   10   11
CONECT   12   13   13   14
CONECT   14   40
CONECT   23   41   42
CONECT   24   43
CONECT   25   44
CONECT   26   45
CONECT   27   46
CONECT   28   47
CONECT   29   48
CONECT   30   49
CONECT   31   50
CONECT   32   51
END
Download

SMILES for HMDB0302648 (Nitrogenase)

[NH2-].[SH-].[SH-].[SH-].[SH-].[SH-].[SH-].[SH-].[SH-].[SH-].[Fe].[Fe].[Fe].[Fe].[Fe].[Fe].[Fe].[Mo].OC(=O)C(O)(CCC([O-])=O)CC([O-])=O
Download

INCHI for HMDB0302648 (Nitrogenase)

InChI=1S/C7H10O7.7Fe.Mo.H2N.9H2S/c8-4(9)1-2-7(14,6(12)13)3-5(10)11;;;;;;;;;;;;;;;;;;/h14H,1-3H2,(H,8,9)(H,10,11)(H,12,13);;;;;;;;;10*1H2/q;;;;;;;;;-1;;;;;;;;;/p-11
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View in JSmolView Stereo Labels
Synonyms
ValueSource
2-Hydroxybutane-1,2,4-tricarboxylate heptairon molybdenum sulphane azanide octasulphanideGenerator
2-Hydroxybutane-1,2,4-tricarboxylic acid heptairon molybdenum sulfane azanide octasulfanideGenerator
2-Hydroxybutane-1,2,4-tricarboxylic acid heptairon molybdenum sulphane azanide octasulphanideGenerator
Chemical FormulaC7H19Fe7MoNO7S9
Average Molecular Weight1004.67
Monoisotopic Molecular Weight1006.314790954
IUPAC Name3-carboxy-3-hydroxyhexanedioate heptairon molybdenum azanide nonasulfanide
Traditional Name3-hydroxy-3-carboxyadipate heptairon molybdenum azanide nonasulfanide
CAS Registry NumberNot Available
SMILES
[NH2-].[SH-].[SH-].[SH-].[SH-].[SH-].[SH-].[SH-].[SH-].[SH-].[Fe].[Fe].[Fe].[Fe].[Fe].[Fe].[Fe].[Mo].OC(=O)C(O)(CCC([O-])=O)CC([O-])=O
InChI Identifier
InChI=1S/C7H10O7.7Fe.Mo.H2N.9H2S/c8-4(9)1-2-7(14,6(12)13)3-5(10)11;;;;;;;;;;;;;;;;;;/h14H,1-3H2,(H,8,9)(H,10,11)(H,12,13);;;;;;;;;10*1H2/q;;;;;;;;;-1;;;;;;;;;/p-11
InChI KeyOUNCJAISYHCMSR-UHFFFAOYSA-C
Chemical Taxonomy
Description Belongs to the class of organic compounds known as tricarboxylic acids and derivatives. These are carboxylic acids containing exactly three carboxyl groups.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassCarboxylic acids and derivatives
Sub ClassTricarboxylic acids and derivatives
Direct ParentTricarboxylic acids and derivatives
Alternative Parents
Substituents
  • Tricarboxylic acid or derivatives
  • Alpha-hydroxy acid
  • Hydroxy acid
  • Tertiary alcohol
  • Carboxylic acid
  • Organic transition metal salt
  • Hydrocarbon derivative
  • Organic oxide
  • Organooxygen compound
  • Organic oxygen compound
  • Alcohol
  • Carbonyl group
  • Organic nitrogen compound
  • Organic salt
  • Organic anion
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
Source
ProcessNot Available
RoleNot Available
Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
logP-1ChemAxon
pKa (Strongest Acidic)3.09ChemAxon
pKa (Strongest Basic)-4.1ChemAxon
Physiological Charge-3ChemAxon
Hydrogen Acceptor Count7ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area137.79 ŲChemAxon
Rotatable Bond Count6ChemAxon
Refractivity62.05 m³·mol⁻¹ChemAxon
Polarizability16.72 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
AllCCS[M+H]+199.89232859911
AllCCS[M+H-H2O]+199.20532859911
AllCCS[M+Na]+200.66432859911
AllCCS[M+NH4]+200.49732859911
AllCCS[M-H]-299.46232859911
AllCCS[M+Na-2H]-304.4332859911
AllCCS[M+HCOO]-309.8932859911

Predicted Kovats Retention Indices

Not Available
Spectra

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Nitrogenase 10V, Positive-QTOFsplash10-0a4i-9000000000-935184df83de846efe562016-08-02Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Nitrogenase 20V, Positive-QTOFsplash10-0a4i-9000000000-935184df83de846efe562016-08-02Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Nitrogenase 40V, Positive-QTOFsplash10-0a4i-9000000000-935184df83de846efe562016-08-02Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Nitrogenase 10V, Negative-QTOFsplash10-0a4i-9000000000-f3ed0469523cac8972a12016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Nitrogenase 20V, Negative-QTOFsplash10-0a4i-9000000000-f3ed0469523cac8972a12016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Nitrogenase 40V, Negative-QTOFsplash10-0a4i-9000000000-f3ed0469523cac8972a12016-08-03Wishart LabView Spectrum
Biological Properties
Cellular LocationsNot Available
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB005600
KNApSAcK IDNot Available
Chemspider ID4925366
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound25199882
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General ReferencesNot Available