data_5DD # _chem_comp.id 5DD _chem_comp.name "[(2~{R},3~{S},4~{S})-5-[(4~{a}~{R})-7,8-dimethyl-2,4-bis(oxidanylidene)-4~{a},5-dihydropyrimido[4,5-b]quinolin-10-yl]-2,3,4-tris(oxidanyl)pentyl] dihydrogen phosphate" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C18 H24 N3 O9 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2018-10-31 _chem_comp.pdbx_modified_date 2019-05-24 _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 457.372 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 5DD _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 6I25 _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site EBI # # 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 5DD O3P O1 O 0 1 N N N -37.754 46.138 5.330 7.490 0.352 -1.669 O3P 5DD 1 5DD P P1 P 0 1 N N N -37.105 45.034 4.530 6.675 0.090 -0.306 P 5DD 2 5DD O1P O2 O 0 1 N N N -35.646 44.869 4.930 7.129 -1.318 0.329 O1P 5DD 3 5DD O2P O3 O 0 1 N N N -37.196 45.363 3.051 6.959 1.179 0.655 O2P 5DD 4 5DD "O5'" O4 O 0 1 N N N -37.915 43.666 4.825 5.097 0.052 -0.622 "O5'" 5DD 5 5DD "C5'" C1 C 0 1 N N N -37.504 42.399 4.328 4.101 -0.059 0.397 "C5'" 5DD 6 5DD "C4'" C2 C 0 1 N N R -36.389 41.825 5.197 2.712 -0.066 -0.245 "C4'" 5DD 7 5DD "O4'" O5 O 0 1 N N N -35.224 42.662 5.122 2.565 -1.240 -1.047 "O4'" 5DD 8 5DD "C3'" C3 C 0 1 N N S -36.867 41.692 6.643 1.644 -0.059 0.850 "C3'" 5DD 9 5DD "O3'" O6 O 0 1 N N N -38.124 41.002 6.625 1.791 1.114 1.652 "O3'" 5DD 10 5DD "C2'" C4 C 0 1 N N S -35.859 40.942 7.528 0.255 -0.067 0.207 "C2'" 5DD 11 5DD "O2'" O7 O 0 1 N N N -36.354 40.772 8.855 0.108 -1.240 -0.595 "O2'" 5DD 12 5DD "C1'" C5 C 0 1 N N N -35.566 39.582 6.918 -0.813 -0.060 1.302 "C1'" 5DD 13 5DD N10 N1 N 0 1 N N N -35.118 38.620 7.912 -2.143 -0.036 0.687 N10 5DD 14 5DD C9A C6 C 0 1 Y N N -36.048 37.928 8.677 -2.707 1.181 0.294 C9A 5DD 15 5DD C9 C7 C 0 1 Y N N -37.314 38.451 8.912 -2.172 2.374 0.762 C9 5DD 16 5DD C8 C8 C 0 1 Y N N -38.220 37.713 9.663 -2.721 3.578 0.367 C8 5DD 17 5DD C8M C9 C 0 1 N N N -39.586 38.250 9.959 -2.141 4.872 0.876 C8M 5DD 18 5DD C7 C10 C 0 1 Y N N -37.847 36.376 10.184 -3.803 3.598 -0.495 C7 5DD 19 5DD C7M C11 C 0 1 N N N -38.834 35.584 10.993 -4.396 4.915 -0.927 C7M 5DD 20 5DD C6 C12 C 0 1 Y N N -36.592 35.857 9.924 -4.341 2.412 -0.961 C6 5DD 21 5DD C5A C13 C 0 1 Y N N -35.677 36.577 9.175 -3.800 1.206 -0.565 C5A 5DD 22 5DD C10 C14 C 0 1 N N N -33.802 38.179 7.888 -2.820 -1.194 0.496 C10 5DD 23 5DD N1 N2 N 0 1 N N N -33.037 38.732 6.928 -2.220 -2.337 0.700 N1 5DD 24 5DD C4A C15 C 0 1 N N R -33.289 37.119 8.846 -4.252 -1.139 0.043 C4A 5DD 25 5DD C4 C16 C 0 1 N N N -31.919 36.714 8.439 -4.723 -2.483 -0.421 C4 5DD 26 5DD O4 O8 O 0 1 N N N -31.379 35.828 9.132 -5.777 -2.576 -1.013 O4 5DD 27 5DD N3 N3 N 0 1 N N N -31.229 37.371 7.490 -3.992 -3.587 -0.190 N3 5DD 28 5DD C2 C17 C 0 1 N N N -31.773 38.340 6.743 -2.799 -3.511 0.423 C2 5DD 29 5DD O2 O9 O 0 1 N N N -31.106 38.905 5.855 -2.228 -4.539 0.735 O2 5DD 30 5DD C1 C18 C 0 1 N N N -34.305 35.985 8.907 -4.403 -0.089 -1.053 C1 5DD 31 5DD H1 H1 H 0 1 N N N -38.083 46.806 4.740 8.449 0.387 -1.554 H1 5DD 32 5DD H2 H2 H 0 1 N N N -35.092 45.006 4.171 6.972 -2.078 -0.247 H2 5DD 33 5DD H3 H3 H 0 1 N N N -38.362 41.710 4.337 4.250 -0.985 0.951 H3 5DD 34 5DD H4 H4 H 0 1 N N N -37.137 42.515 3.297 4.182 0.789 1.078 H4 5DD 35 5DD H5 H5 H 0 1 N N N -36.143 40.820 4.822 2.597 0.819 -0.871 H5 5DD 36 5DD H6 H6 H 0 1 N N N -34.536 42.297 5.666 2.656 -2.067 -0.555 H6 5DD 37 5DD H7 H7 H 0 1 N N N -37.005 42.702 7.057 1.759 -0.944 1.476 H7 5DD 38 5DD H8 H8 H 0 1 N N N -38.445 40.905 7.514 1.700 1.941 1.159 H8 5DD 39 5DD H9 H9 H 0 1 N N N -34.924 41.521 7.552 0.140 0.818 -0.419 H9 5DD 40 5DD H10 H10 H 0 1 N N N -35.710 40.307 9.376 0.204 -2.067 -0.103 H10 5DD 41 5DD H11 H11 H 0 1 N N N -36.483 39.201 6.444 -0.712 -0.956 1.914 H11 5DD 42 5DD H12 H12 H 0 1 N N N -34.780 39.697 6.157 -0.687 0.824 1.928 H12 5DD 43 5DD H13 H13 H 0 1 N N N -37.589 39.417 8.516 -1.327 2.361 1.434 H13 5DD 44 5DD H14 H14 H 0 1 N N N -40.282 37.943 9.164 -1.361 5.213 0.195 H14 5DD 45 5DD H15 H15 H 0 1 N N N -39.934 37.854 10.924 -2.927 5.625 0.933 H15 5DD 46 5DD H16 H16 H 0 1 N N N -39.546 39.348 10.006 -1.715 4.715 1.867 H16 5DD 47 5DD H17 H17 H 0 1 N N N -39.435 34.952 10.323 -3.898 5.257 -1.834 H17 5DD 48 5DD H18 H18 H 0 1 N N N -38.294 34.948 11.709 -5.461 4.786 -1.122 H18 5DD 49 5DD H19 H19 H 0 1 N N N -39.496 36.272 11.540 -4.258 5.652 -0.137 H19 5DD 50 5DD H20 H20 H 0 1 N N N -36.324 34.884 10.308 -5.185 2.430 -1.634 H20 5DD 51 5DD H21 H21 H 0 1 N N N -33.231 37.571 9.847 -4.869 -0.842 0.891 H21 5DD 52 5DD H22 H22 H 0 1 N N N -30.272 37.126 7.336 -4.331 -4.452 -0.468 H22 5DD 53 5DD H23 H23 H 0 1 N N N -34.315 35.445 7.949 -5.459 0.059 -1.276 H23 5DD 54 5DD H24 H24 H 0 1 N N N -34.037 35.290 9.717 -3.879 -0.419 -1.950 H24 5DD 55 # # 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 5DD O2P P DOUB N N 1 5DD "C5'" "O5'" SING N N 2 5DD "C5'" "C4'" SING N N 3 5DD P "O5'" SING N N 4 5DD P O1P SING N N 5 5DD P O3P SING N N 6 5DD "O4'" "C4'" SING N N 7 5DD "C4'" "C3'" SING N N 8 5DD O2 C2 DOUB N N 9 5DD "O3'" "C3'" SING N N 10 5DD "C3'" "C2'" SING N N 11 5DD C2 N1 SING N N 12 5DD C2 N3 SING N N 13 5DD "C1'" "C2'" SING N N 14 5DD "C1'" N10 SING N N 15 5DD N1 C10 DOUB N N 16 5DD N3 C4 SING N N 17 5DD "C2'" "O2'" SING N N 18 5DD C10 N10 SING N N 19 5DD C10 C4A SING N N 20 5DD N10 C9A SING N N 21 5DD C4 C4A SING N N 22 5DD C4 O4 DOUB N N 23 5DD C9A C9 DOUB Y N 24 5DD C9A C5A SING Y N 25 5DD C4A C1 SING N N 26 5DD C1 C5A SING N N 27 5DD C9 C8 SING Y N 28 5DD C5A C6 DOUB Y N 29 5DD C8 C8M SING N N 30 5DD C8 C7 DOUB Y N 31 5DD C6 C7 SING Y N 32 5DD C7 C7M SING N N 33 5DD O3P H1 SING N N 34 5DD O1P H2 SING N N 35 5DD "C5'" H3 SING N N 36 5DD "C5'" H4 SING N N 37 5DD "C4'" H5 SING N N 38 5DD "O4'" H6 SING N N 39 5DD "C3'" H7 SING N N 40 5DD "O3'" H8 SING N N 41 5DD "C2'" H9 SING N N 42 5DD "O2'" H10 SING N N 43 5DD "C1'" H11 SING N N 44 5DD "C1'" H12 SING N N 45 5DD C9 H13 SING N N 46 5DD C8M H14 SING N N 47 5DD C8M H15 SING N N 48 5DD C8M H16 SING N N 49 5DD C7M H17 SING N N 50 5DD C7M H18 SING N N 51 5DD C7M H19 SING N N 52 5DD C6 H20 SING N N 53 5DD C4A H21 SING N N 54 5DD N3 H22 SING N N 55 5DD C1 H23 SING N N 56 5DD C1 H24 SING N N 57 # # 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 5DD InChI InChI 1.03 "InChI=1S/C18H24N3O9P/c1-8-3-10-5-11-16(19-18(26)20-17(11)25)21(12(10)4-9(8)2)6-13(22)15(24)14(23)7-30-31(27,28)29/h3-4,11,13-15,22-24H,5-7H2,1-2H3,(H,20,25,26)(H2,27,28,29)/t11-,13+,14-,15+/m1/s1" 5DD InChIKey InChI 1.03 MPTDYDRCOLGCLP-BEAPCOKYSA-N 5DD SMILES_CANONICAL CACTVS 3.385 "Cc1cc2C[C@H]3C(=O)NC(=O)N=C3N(C[C@H](O)[C@H](O)[C@H](O)CO[P](O)(O)=O)c2cc1C" 5DD SMILES CACTVS 3.385 "Cc1cc2C[CH]3C(=O)NC(=O)N=C3N(C[CH](O)[CH](O)[CH](O)CO[P](O)(O)=O)c2cc1C" 5DD SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)[C@@H]3C2)C[C@@H]([C@@H]([C@@H](COP(=O)(O)O)O)O)O" 5DD SMILES "OpenEye OEToolkits" 2.0.6 "Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3C2)CC(C(C(COP(=O)(O)O)O)O)O" # _pdbx_chem_comp_identifier.comp_id 5DD _pdbx_chem_comp_identifier.type "SYSTEMATIC NAME" _pdbx_chem_comp_identifier.program "OpenEye OEToolkits" _pdbx_chem_comp_identifier.program_version 2.0.6 _pdbx_chem_comp_identifier.identifier "[(2~{R},3~{S},4~{S})-5-[(4~{a}~{R})-7,8-dimethyl-2,4-bis(oxidanylidene)-4~{a},5-dihydropyrimido[4,5-b]quinolin-10-yl]-2,3,4-tris(oxidanyl)pentyl] dihydrogen phosphate" # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site 5DD "Create component" 2018-10-31 EBI 5DD "Initial release" 2019-05-29 RCSB ##