data_1L3
#

_chem_comp.id                                   1L3
_chem_comp.name                                 Menaquinone-4
_chem_comp.type                                 non-polymer
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C31 H40 O2"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        "vitamin K2"
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2021-07-02
_chem_comp.pdbx_modified_date                   2022-04-01
_chem_comp.pdbx_ambiguous_flag                  N
_chem_comp.pdbx_release_status                  REL
_chem_comp.pdbx_replaced_by                     ?
_chem_comp.pdbx_replaces                        ?
_chem_comp.formula_weight                       444.648
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    1L3
_chem_comp.pdbx_model_coordinates_details       ?
_chem_comp.pdbx_model_coordinates_missing_flag  N
_chem_comp.pdbx_ideal_coordinates_details       Corina
_chem_comp.pdbx_ideal_coordinates_missing_flag  N
_chem_comp.pdbx_model_coordinates_db_code       7F4V
_chem_comp.pdbx_subcomponent_list               ?
_chem_comp.pdbx_processing_site                 PDBJ
#   #
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.alt_atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.charge
_chem_comp_atom.pdbx_align
_chem_comp_atom.pdbx_aromatic_flag
_chem_comp_atom.pdbx_leaving_atom_flag
_chem_comp_atom.pdbx_stereo_config
_chem_comp_atom.model_Cartn_x
_chem_comp_atom.model_Cartn_y
_chem_comp_atom.model_Cartn_z
_chem_comp_atom.pdbx_model_Cartn_x_ideal
_chem_comp_atom.pdbx_model_Cartn_y_ideal
_chem_comp_atom.pdbx_model_Cartn_z_ideal
_chem_comp_atom.pdbx_component_atom_id
_chem_comp_atom.pdbx_component_comp_id
_chem_comp_atom.pdbx_ordinal
1L3  C10  C1   C  0  1  Y  N  N  120.112  173.628  158.236  -6.966   2.373  -1.068  C10  1L3   1  
1L3  C15  C2   C  0  1  N  N  N  126.658  173.462  159.418  -2.700  -2.290   0.250  C15  1L3   2  
1L3  C17  C3   C  0  1  N  N  N  127.853  173.018  157.250  -2.212  -2.903   2.562  C17  1L3   3  
1L3  C20  C4   C  0  1  N  N  N  130.467  170.542  159.931   1.459  -0.487   1.001  C20  1L3   4  
1L3  C21  C5   C  0  1  N  N  N  130.728  170.047  161.152   1.796   0.523   0.237  C21  1L3   5  
1L3  C22  C6   C  0  1  N  N  N  130.194  170.761  162.451   0.729   1.336  -0.449  C22  1L3   6  
1L3  C24  C7   C  0  1  N  N  N  133.061  169.135  161.410   3.769   0.206  -1.230  C24  1L3   7  
1L3  C26  C8   C  0  1  N  N  N  134.999  167.690  160.680   6.110  -0.397  -1.576  C26  1L3   8  
1L3  C28  C9   C  0  1  N  N  N  135.892  166.394  160.844   7.579  -0.064  -1.581  C28  1L3   9  
1L3  C01  C10  C  0  1  N  N  N  124.005  175.277  161.131  -5.429  -2.381  -1.944  C01  1L3  10  
1L3  C02  C11  C  0  1  N  N  N  123.536  174.709  159.797  -5.496  -1.164  -1.057  C02  1L3  11  
1L3  C03  C12  C  0  1  N  N  N  124.466  174.424  158.667  -4.896  -1.185   0.140  C03  1L3  12  
1L3  C04  C13  C  0  1  N  N  N  123.913  173.857  157.383  -4.943  -0.011   1.032  C04  1L3  13  
1L3  C06  C14  C  0  1  Y  N  N  122.371  173.584  157.255  -5.660   1.209   0.602  C06  1L3  14  
1L3  C07  C15  C  0  1  Y  N  N  121.828  173.060  156.072  -5.719   2.329   1.423  C07  1L3  15  
1L3  C08  C16  C  0  1  Y  N  N  120.450  172.818  155.966  -6.405   3.457   1.001  C08  1L3  16  
1L3  C09  C17  C  0  1  Y  N  N  119.580  173.114  157.051  -7.020   3.480  -0.236  C09  1L3  17  
1L3  C11  C18  C  0  1  Y  N  N  121.497  173.874  158.335  -6.290   1.231  -0.655  C11  1L3  18  
1L3  C12  C19  C  0  1  N  N  N  122.071  174.451  159.658  -6.221   0.034  -1.521  C12  1L3  19  
1L3  C14  C20  C  0  1  N  N  N  125.981  174.689  158.803  -4.163  -2.425   0.583  C14  1L3  20  
1L3  C16  C21  C  0  1  N  N  N  127.514  172.700  158.704  -1.798  -2.451   1.185  C16  1L3  21  
1L3  C18  C22  C  0  1  N  N  N  128.162  171.475  159.402  -0.345  -2.184   0.885  C18  1L3  22  
1L3  C19  C23  C  0  1  N  N  N  129.626  171.814  159.757   0.007  -0.754   1.301  C19  1L3  23  
1L3  C23  C24  C  0  1  N  N  N  131.592  168.765  161.258   3.249   0.871   0.046  C23  1L3  24  
1L3  C25  C25  C  0  1  N  N  N  133.971  167.879  161.520   5.223   0.554  -1.422  C25  1L3  25  
1L3  C27  C26  C  0  1  N  N  N  135.314  168.718  159.603   5.661  -1.825  -1.747  C27  1L3  26  
1L3  C29  C27  C  0  1  N  N  N  135.680  165.340  159.754   8.152  -0.259  -0.175  C29  1L3  27  
1L3  C30  C28  C  0  1  N  N  N  134.237  164.832  159.754   9.621   0.075  -0.181  C30  1L3  28  
1L3  C31  C29  C  0  1  N  N  N  133.816  163.952  158.861  10.099   0.941   0.678  C31  1L3  29  
1L3  C32  C30  C  0  1  N  N  N  134.772  163.390  157.778  11.538   1.379   0.584  C32  1L3  30  
1L3  C33  C31  C  0  1  N  N  N  132.344  163.461  158.893   9.211   1.500   1.759  C33  1L3  31  
1L3  O05  O1   O  0  1  N  N  N  124.646  173.618  156.492  -4.394  -0.045   2.115  O05  1L3  32  
1L3  O13  O2   O  0  1  N  N  N  121.383  174.709  160.560  -6.760   0.038  -2.610  O13  1L3  33  
1L3  H1   H1   H  0  1  N  N  N  119.464  173.837  159.074  -7.452   2.396  -2.033  H1   1L3  34  
1L3  H2   H2   H  0  1  N  N  N  126.447  173.200  160.444  -2.395  -2.061  -0.761  H2   1L3  35  
1L3  H3   H3   H  0  1  N  N  N  127.301  173.915  156.932  -1.338  -2.933   3.213  H3   1L3  36  
1L3  H4   H4   H  0  1  N  N  N  128.934  173.200  157.157  -2.944  -2.206   2.968  H4   1L3  37  
1L3  H5   H5   H  0  1  N  N  N  127.568  172.168  156.613  -2.653  -3.898   2.500  H5   1L3  38  
1L3  H6   H6   H  0  1  N  N  N  130.855  170.037  159.058   2.223  -1.128   1.416  H6   1L3  39  
1L3  H7   H7   H  0  1  N  N  N  130.517  170.198  163.339   0.120   1.842   0.299  H7   1L3  40  
1L3  H8   H8   H  0  1  N  N  N  130.597  171.783  162.499   1.197   2.076  -1.098  H8   1L3  41  
1L3  H9   H9   H  0  1  N  N  N  129.095  170.801  162.422   0.098   0.677  -1.046  H9   1L3  42  
1L3  H10  H10  H  0  1  N  N  N  133.372  169.723  160.533   3.663  -0.876  -1.145  H10  1L3  43  
1L3  H11  H11  H  0  1  N  N  N  133.182  169.742  162.320   3.194   0.561  -2.085  H11  1L3  44  
1L3  H12  H12  H  0  1  N  N  N  135.659  165.936  161.816   8.099  -0.721  -2.279  H12  1L3  45  
1L3  H13  H13  H  0  1  N  N  N  136.949  166.699  160.827   7.716   0.973  -1.888  H13  1L3  46  
1L3  H14  H14  H  0  1  N  N  N  123.142  175.400  161.802  -6.276  -3.033  -1.731  H14  1L3  47  
1L3  H15  H15  H  0  1  N  N  N  124.729  174.587  161.589  -5.462  -2.072  -2.988  H15  1L3  48  
1L3  H16  H16  H  0  1  N  N  N  124.483  176.254  160.966  -4.500  -2.918  -1.753  H16  1L3  49  
1L3  H17  H17  H  0  1  N  N  N  122.476  172.841  155.236  -5.237   2.318   2.390  H17  1L3  50  
1L3  H18  H18  H  0  1  N  N  N  120.047  172.404  155.054  -6.451   4.327   1.639  H18  1L3  51  
1L3  H19  H19  H  0  1  N  N  N  118.518  172.943  156.960  -7.545   4.367  -0.557  H19  1L3  52  
1L3  H20  H20  H  0  1  N  N  N  126.410  174.885  157.809  -4.575  -3.293   0.068  H20  1L3  53  
1L3  H21  H21  H  0  1  N  N  N  126.144  175.562  159.452  -4.281  -2.552   1.659  H21  1L3  54  
1L3  H22  H22  H  0  1  N  N  N  127.606  171.237  160.321   0.276  -2.887   1.441  H22  1L3  55  
1L3  H23  H23  H  0  1  N  N  N  128.138  170.609  158.724  -0.166  -2.306  -0.183  H23  1L3  56  
1L3  H24  H24  H  0  1  N  N  N  130.059  172.422  158.949  -0.172  -0.632   2.369  H24  1L3  57  
1L3  H25  H25  H  0  1  N  N  N  129.644  172.386  160.696  -0.614  -0.051   0.746  H25  1L3  58  
1L3  H26  H26  H  0  1  N  N  N  131.271  168.182  162.134   3.355   1.953  -0.040  H26  1L3  59  
1L3  H27  H27  H  0  1  N  N  N  131.461  168.162  160.348   3.824   0.516   0.901  H27  1L3  60  
1L3  H28  H28  H  0  1  N  N  N  133.771  167.145  162.287   5.533   1.589  -1.432  H28  1L3  61  
1L3  H29  H29  H  0  1  N  N  N  134.583  169.538  159.653   5.512  -2.280  -0.768  H29  1L3  62  
1L3  H30  H30  H  0  1  N  N  N  136.326  169.119  159.764   4.724  -1.847  -2.304  H30  1L3  63  
1L3  H31  H31  H  0  1  N  N  N  135.262  168.240  158.614   6.421  -2.382  -2.295  H31  1L3  64  
1L3  H32  H32  H  0  1  N  N  N  136.359  164.494  159.935   7.633   0.398   0.523  H32  1L3  65  
1L3  H33  H33  H  0  1  N  N  N  135.904  165.786  158.774   8.016  -1.296   0.132  H33  1L3  66  
1L3  H34  H34  H  0  1  N  N  N  133.547  165.200  160.499  10.280  -0.400  -0.892  H34  1L3  67  
1L3  H35  H35  H  0  1  N  N  N  135.768  163.840  157.898  12.160   0.715   1.185  H35  1L3  68  
1L3  H36  H36  H  0  1  N  N  N  134.848  162.298  157.887  11.863   1.339  -0.456  H36  1L3  69  
1L3  H37  H37  H  0  1  N  N  N  134.378  163.633  156.780  11.632   2.400   0.955  H37  1L3  70  
1L3  H38  H38  H  0  1  N  N  N  131.810  163.956  159.717   8.244   0.996   1.731  H38  1L3  71  
1L3  H39  H39  H  0  1  N  N  N  131.855  163.706  157.939   9.676   1.339   2.731  H39  1L3  72  
1L3  H40  H40  H  0  1  N  N  N  132.324  162.372  159.046   9.069   2.568   1.597  H40  1L3  73  
#   #
loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.value_order
_chem_comp_bond.pdbx_aromatic_flag
_chem_comp_bond.pdbx_stereo_config
_chem_comp_bond.pdbx_ordinal
1L3  C08  C07  DOUB  Y  N   1  
1L3  C08  C09  SING  Y  N   2  
1L3  C07  C06  SING  Y  N   3  
1L3  O05  C04  DOUB  N  N   4  
1L3  C09  C10  DOUB  Y  N   5  
1L3  C17  C16  SING  N  N   6  
1L3  C06  C04  SING  N  N   7  
1L3  C06  C11  DOUB  Y  N   8  
1L3  C04  C03  SING  N  N   9  
1L3  C32  C31  SING  N  N  10  
1L3  C10  C11  SING  Y  N  11  
1L3  C11  C12  SING  N  N  12  
1L3  C03  C14  SING  N  N  13  
1L3  C03  C02  DOUB  N  N  14  
1L3  C16  C18  SING  N  N  15  
1L3  C16  C15  DOUB  N  E  16  
1L3  C14  C15  SING  N  N  17  
1L3  C31  C33  SING  N  N  18  
1L3  C31  C30  DOUB  N  N  19  
1L3  C18  C19  SING  N  N  20  
1L3  C27  C26  SING  N  N  21  
1L3  C12  C02  SING  N  N  22  
1L3  C12  O13  DOUB  N  N  23  
1L3  C29  C30  SING  N  N  24  
1L3  C29  C28  SING  N  N  25  
1L3  C19  C20  SING  N  N  26  
1L3  C02  C01  SING  N  N  27  
1L3  C20  C21  DOUB  N  E  28  
1L3  C26  C28  SING  N  N  29  
1L3  C26  C25  DOUB  N  E  30  
1L3  C21  C23  SING  N  N  31  
1L3  C21  C22  SING  N  N  32  
1L3  C23  C24  SING  N  N  33  
1L3  C24  C25  SING  N  N  34  
1L3  C10  H1   SING  N  N  35  
1L3  C15  H2   SING  N  N  36  
1L3  C17  H3   SING  N  N  37  
1L3  C17  H4   SING  N  N  38  
1L3  C17  H5   SING  N  N  39  
1L3  C20  H6   SING  N  N  40  
1L3  C22  H7   SING  N  N  41  
1L3  C22  H8   SING  N  N  42  
1L3  C22  H9   SING  N  N  43  
1L3  C24  H10  SING  N  N  44  
1L3  C24  H11  SING  N  N  45  
1L3  C28  H12  SING  N  N  46  
1L3  C28  H13  SING  N  N  47  
1L3  C01  H14  SING  N  N  48  
1L3  C01  H15  SING  N  N  49  
1L3  C01  H16  SING  N  N  50  
1L3  C07  H17  SING  N  N  51  
1L3  C08  H18  SING  N  N  52  
1L3  C09  H19  SING  N  N  53  
1L3  C14  H20  SING  N  N  54  
1L3  C14  H21  SING  N  N  55  
1L3  C18  H22  SING  N  N  56  
1L3  C18  H23  SING  N  N  57  
1L3  C19  H24  SING  N  N  58  
1L3  C19  H25  SING  N  N  59  
1L3  C23  H26  SING  N  N  60  
1L3  C23  H27  SING  N  N  61  
1L3  C25  H28  SING  N  N  62  
1L3  C27  H29  SING  N  N  63  
1L3  C27  H30  SING  N  N  64  
1L3  C27  H31  SING  N  N  65  
1L3  C29  H32  SING  N  N  66  
1L3  C29  H33  SING  N  N  67  
1L3  C30  H34  SING  N  N  68  
1L3  C32  H35  SING  N  N  69  
1L3  C32  H36  SING  N  N  70  
1L3  C32  H37  SING  N  N  71  
1L3  C33  H38  SING  N  N  72  
1L3  C33  H39  SING  N  N  73  
1L3  C33  H40  SING  N  N  74  
#   #
loop_
_pdbx_chem_comp_descriptor.comp_id
_pdbx_chem_comp_descriptor.type
_pdbx_chem_comp_descriptor.program
_pdbx_chem_comp_descriptor.program_version
_pdbx_chem_comp_descriptor.descriptor
1L3  InChI             InChI                 1.03   "InChI=1S/C31H40O2/c1-22(2)12-9-13-23(3)14-10-15-24(4)16-11-17-25(5)20-21-27-26(6)30(32)28-18-7-8-19-29(28)31(27)33/h7-8,12,14,16,18-20H,9-11,13,15,17,21H2,1-6H3/b23-14+,24-16+,25-20+"  
1L3  InChIKey          InChI                 1.03   DKHGMERMDICWDU-GHDNBGIDSA-N  
1L3  SMILES_CANONICAL  CACTVS                3.385  "CC(C)=CCC\C(C)=C\CCC(/C)=C/CCC(/C)=C/CC1=C(C)C(=O)c2ccccc2C1=O"  
1L3  SMILES            CACTVS                3.385  "CC(C)=CCCC(C)=CCCC(C)=CCCC(C)=CCC1=C(C)C(=O)c2ccccc2C1=O"  
1L3  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.7  "CC1=C(C(=O)c2ccccc2C1=O)C/C=C(\C)/CC/C=C(\C)/CC/C=C(\C)/CCC=C(C)C"  
1L3  SMILES            "OpenEye OEToolkits"  2.0.7  "CC1=C(C(=O)c2ccccc2C1=O)CC=C(C)CCC=C(C)CCC=C(C)CCC=C(C)C"  
#
_pdbx_chem_comp_identifier.comp_id          1L3
_pdbx_chem_comp_identifier.type             "SYSTEMATIC NAME"
_pdbx_chem_comp_identifier.program          "OpenEye OEToolkits"
_pdbx_chem_comp_identifier.program_version  2.0.7
_pdbx_chem_comp_identifier.identifier       "2-methyl-3-[(2~{E},6~{E},10~{E})-3,7,11,15-tetramethylhexadeca-2,6,10,14-tetraenyl]naphthalene-1,4-dione"
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     1L3
_pdbx_chem_comp_synonyms.name        "vitamin K2"
_pdbx_chem_comp_synonyms.provenance  PUBCHEM
_pdbx_chem_comp_synonyms.type        ?
#   #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
1L3  "Create component"  2021-07-02  PDBJ  
1L3  "Initial release"   2022-04-06  RCSB  
##
