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 ##