data_DM5 # _chem_comp.id DM5 _chem_comp.name IDARUBICIN _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAD _chem_comp.formula "C26 H27 N O9" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms 4-DEMETHOXY-DAUNORUBICIN _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 1999-07-08 _chem_comp.pdbx_modified_date 2020-06-17 _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 497.494 _chem_comp.one_letter_code ? _chem_comp.three_letter_code DM5 _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag N _chem_comp.pdbx_ideal_coordinates_details ? _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 1D67 _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site RCSB # # 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 DM5 C1 C1 C 0 1 Y N N -12.748 18.560 4.966 -0.481 -0.601 -6.318 C1 DM5 1 DM5 C2 C2 C 0 1 Y N N -11.592 19.243 4.982 -1.668 -0.492 -7.021 C2 DM5 2 DM5 C3 C3 C 0 1 Y N N -10.447 18.619 4.913 -2.804 0.000 -6.406 C3 DM5 3 DM5 C4 C4 C 0 1 Y N N -10.278 17.295 4.828 -2.771 0.390 -5.079 C4 DM5 4 DM5 C5 C5 C 0 1 Y N N -11.456 16.522 4.865 -1.586 0.286 -4.357 C5 DM5 5 DM5 C6 C6 C 0 1 N N N -11.392 14.986 4.813 -1.531 0.695 -2.936 C6 DM5 6 DM5 O6 O6 O 0 1 N N N -10.354 14.385 4.723 -2.431 1.353 -2.450 O6 DM5 7 DM5 C7 C7 C 0 1 Y N N -12.717 14.290 4.834 -0.372 0.296 -2.117 C7 DM5 8 DM5 C8 C8 C 0 1 Y N N -12.674 12.891 4.781 -0.404 0.408 -0.730 C8 DM5 9 DM5 O8 O8 O 0 1 N N N -11.516 12.167 4.781 -1.514 0.893 -0.120 O8 DM5 10 DM5 C9 C9 C 0 1 Y N N -13.889 12.147 4.770 0.702 0.024 0.039 C9 DM5 11 DM5 C10 C10 C 0 1 N N S -13.827 10.650 4.886 0.592 0.182 1.534 C10 DM5 12 DM5 O10 O10 O 0 1 N N N -13.215 10.419 6.121 -0.703 -0.244 1.959 O10 DM5 13 DM5 C11 C11 C 0 1 N N N -15.183 10.033 4.649 1.655 -0.653 2.243 C11 DM5 14 DM5 C12 C12 C 0 1 N N S -16.316 10.721 5.467 3.018 -0.330 1.619 C12 DM5 15 DM5 O12 O12 O 0 1 N N N -16.133 10.740 6.876 4.058 -0.924 2.398 O12 DM5 16 DM5 C13 C13 C 0 1 N N N -17.613 10.044 5.040 3.211 1.163 1.567 C13 DM5 17 DM5 O13 O13 O 0 1 N N N -18.301 10.292 3.995 2.941 1.772 0.560 O13 DM5 18 DM5 C14 C14 C 0 1 N N N -18.036 8.857 5.747 3.743 1.896 2.772 C14 DM5 19 DM5 C15 C15 C 0 1 N N N -16.412 12.122 4.897 3.045 -0.902 0.203 C15 DM5 20 DM5 C16 C16 C 0 1 Y N N -15.099 12.829 4.818 1.827 -0.466 -0.570 C16 DM5 21 DM5 C17 C17 C 0 1 Y N N -15.082 14.273 4.886 1.877 -0.582 -1.967 C17 DM5 22 DM5 O17 O17 O 0 1 N N N -16.297 14.980 4.781 2.995 -1.066 -2.563 O17 DM5 23 DM5 C18 C18 C 0 1 Y N N -13.881 14.966 4.876 0.787 -0.205 -2.745 C18 DM5 24 DM5 C19 C19 C 0 1 N N N -13.917 16.392 4.923 0.829 -0.324 -4.214 C19 DM5 25 DM5 O19 O19 O 0 1 N N N -14.991 17.075 4.934 1.885 -0.510 -4.787 O19 DM5 26 DM5 C20 C20 C 0 1 Y N N -12.708 17.148 4.918 -0.430 -0.214 -4.983 C20 DM5 27 DM5 "C1'" C1* C 0 1 N N R -12.336 9.280 6.459 -1.224 0.789 2.797 "C1'" DM5 28 DM5 "C2'" C2* C 0 1 N N N -11.149 9.678 7.377 -2.724 0.565 3.005 "C2'" DM5 29 DM5 "C3'" C3* C 0 1 N N S -11.674 9.810 8.844 -2.939 -0.811 3.644 "C3'" DM5 30 DM5 "N3'" N3* N 0 1 N N N -10.659 10.591 9.583 -4.358 -0.977 3.989 "N3'" DM5 31 DM5 "C4'" C4* C 0 1 N N S -12.533 8.626 9.282 -2.084 -0.900 4.913 "C4'" DM5 32 DM5 "O4'" O4* O 0 1 N N N -11.476 7.547 9.134 -2.570 0.028 5.883 "O4'" DM5 33 DM5 "C5'" C5* C 0 1 N N S -13.627 8.511 8.348 -0.633 -0.567 4.560 "C5'" DM5 34 DM5 "O5'" O5* O 0 1 N N N -13.193 8.268 7.018 -0.553 0.764 4.055 "O5'" DM5 35 DM5 "C6'" C6* C 0 1 N N N -14.462 7.490 8.876 0.235 -0.688 5.813 "C6'" DM5 36 DM5 H1 H1 H 0 1 N N N -13.689 19.133 4.991 0.403 -0.986 -6.804 H1 DM5 37 DM5 H2 H2 H 0 1 N N N -11.582 20.343 5.053 -1.707 -0.793 -8.058 H2 DM5 38 DM5 H3 H3 H 0 1 N N N -9.550 19.261 4.927 -3.724 0.082 -6.966 H3 DM5 39 DM5 H4 H4 H 0 1 N N N -9.260 16.878 4.735 -3.662 0.775 -4.605 H4 DM5 40 DM5 HO8 HO8 H 0 1 N N N -11.486 11.218 4.745 -2.120 0.148 -0.010 HO8 DM5 41 DM5 H10 H10 H 0 1 N N N -13.220 10.140 4.101 0.728 1.232 1.795 H10 DM5 42 DM5 H111 1H11 H 0 0 N N N -15.429 10.019 3.561 1.670 -0.406 3.305 H111 DM5 43 DM5 H112 2H11 H 0 0 N N N -15.160 8.935 4.845 1.435 -1.713 2.115 H112 DM5 44 DM5 HO12 2HO1 H 0 0 N N N -16.824 11.159 7.374 4.894 -0.695 1.970 HO12 DM5 45 DM5 H141 1H14 H 0 0 N N N -18.984 8.361 5.434 3.814 2.960 2.547 H141 DM5 46 DM5 H142 2H14 H 0 0 N N N -17.210 8.107 5.722 3.068 1.747 3.615 H142 DM5 47 DM5 H143 3H14 H 0 0 N N N -18.087 9.083 6.837 4.731 1.511 3.025 H143 DM5 48 DM5 H151 1H15 H 0 0 N N N -16.911 12.107 3.900 3.941 -0.551 -0.308 H151 DM5 49 DM5 H152 2H15 H 0 0 N N N -17.152 12.729 5.468 3.066 -1.991 0.257 H152 DM5 50 DM5 HO17 7HO1 H 0 0 N N N -16.285 15.928 4.825 2.885 -2.024 -2.626 HO17 DM5 51 DM5 "H1'" H1* H 0 1 N N N -11.821 8.888 5.550 -1.065 1.756 2.320 "H1'" DM5 52 DM5 "H2'1" 1H2* H 0 0 N N N -10.289 8.973 7.293 -3.120 1.339 3.662 "H2'1" DM5 53 DM5 "H2'2" 2H2* H 0 0 N N N -10.627 10.598 7.025 -3.235 0.605 2.043 "H2'2" DM5 54 DM5 "H3'" H3* H 0 1 N N N -12.547 10.440 9.132 -2.639 -1.590 2.943 "H3'" DM5 55 DM5 "HN'1" 1HN* H 0 0 N N N -11.001 10.677 10.539 -4.877 -0.897 3.127 "HN'1" DM5 56 DM5 "HN'2" 2HN* H 0 0 N N N -10.444 11.488 9.148 -4.469 -1.928 4.307 "HN'2" DM5 57 DM5 "H4'" H4* H 0 1 N N N -13.020 8.640 10.284 -2.137 -1.911 5.317 "H4'" DM5 58 DM5 "HO4'" *HO4 H 0 0 N N N -12.010 6.810 9.406 -2.005 -0.060 6.663 "HO4'" DM5 59 DM5 "H5'" H5* H 0 1 N N N -14.189 9.468 8.250 -0.275 -1.264 3.802 "H5'" DM5 60 DM5 "H6'1" 1H6* H 0 0 N N N -15.307 7.401 8.154 1.270 -0.453 5.563 "H6'1" DM5 61 DM5 "H6'2" 2H6* H 0 0 N N N -13.931 6.528 9.068 -0.121 0.008 6.572 "H6'2" DM5 62 DM5 "H6'3" 3H6* H 0 0 N N N -14.785 7.671 9.927 0.177 -1.706 6.199 "H6'3" DM5 63 # # 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 DM5 C1 C2 DOUB Y N 1 DM5 C1 C20 SING Y N 2 DM5 C1 H1 SING N N 3 DM5 C2 C3 SING Y N 4 DM5 C2 H2 SING N N 5 DM5 C3 C4 DOUB Y N 6 DM5 C3 H3 SING N N 7 DM5 C4 C5 SING Y N 8 DM5 C4 H4 SING N N 9 DM5 C5 C6 SING N N 10 DM5 C5 C20 DOUB Y N 11 DM5 C6 O6 DOUB N N 12 DM5 C6 C7 SING N N 13 DM5 C7 C8 DOUB Y N 14 DM5 C7 C18 SING Y N 15 DM5 C8 O8 SING N N 16 DM5 C8 C9 SING Y N 17 DM5 O8 HO8 SING N N 18 DM5 C9 C10 SING N N 19 DM5 C9 C16 DOUB Y N 20 DM5 C10 O10 SING N N 21 DM5 C10 C11 SING N N 22 DM5 C10 H10 SING N N 23 DM5 O10 "C1'" SING N N 24 DM5 C11 C12 SING N N 25 DM5 C11 H111 SING N N 26 DM5 C11 H112 SING N N 27 DM5 C12 O12 SING N N 28 DM5 C12 C13 SING N N 29 DM5 C12 C15 SING N N 30 DM5 O12 HO12 SING N N 31 DM5 C13 O13 DOUB N N 32 DM5 C13 C14 SING N N 33 DM5 C14 H141 SING N N 34 DM5 C14 H142 SING N N 35 DM5 C14 H143 SING N N 36 DM5 C15 C16 SING N N 37 DM5 C15 H151 SING N N 38 DM5 C15 H152 SING N N 39 DM5 C16 C17 SING Y N 40 DM5 C17 O17 SING N N 41 DM5 C17 C18 DOUB Y N 42 DM5 O17 HO17 SING N N 43 DM5 C18 C19 SING N N 44 DM5 C19 O19 DOUB N N 45 DM5 C19 C20 SING N N 46 DM5 "C1'" "C2'" SING N N 47 DM5 "C1'" "O5'" SING N N 48 DM5 "C1'" "H1'" SING N N 49 DM5 "C2'" "C3'" SING N N 50 DM5 "C2'" "H2'1" SING N N 51 DM5 "C2'" "H2'2" SING N N 52 DM5 "C3'" "N3'" SING N N 53 DM5 "C3'" "C4'" SING N N 54 DM5 "C3'" "H3'" SING N N 55 DM5 "N3'" "HN'1" SING N N 56 DM5 "N3'" "HN'2" SING N N 57 DM5 "C4'" "O4'" SING N N 58 DM5 "C4'" "C5'" SING N N 59 DM5 "C4'" "H4'" SING N N 60 DM5 "O4'" "HO4'" SING N N 61 DM5 "C5'" "O5'" SING N N 62 DM5 "C5'" "C6'" SING N N 63 DM5 "C5'" "H5'" SING N N 64 DM5 "C6'" "H6'1" SING N N 65 DM5 "C6'" "H6'2" SING N N 66 DM5 "C6'" "H6'3" SING N N 67 # # 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 DM5 SMILES ACDLabs 10.04 "O=C2c1c(O)c5c(c(O)c1C(=O)c3ccccc23)CC(O)(C(=O)C)CC5OC4OC(C(O)C(N)C4)C" DM5 SMILES_CANONICAL CACTVS 3.341 "C[C@@H]1O[C@H](C[C@H](N)[C@@H]1O)O[C@H]2C[C@@](O)(Cc3c(O)c4C(=O)c5ccccc5C(=O)c4c(O)c23)C(C)=O" DM5 SMILES CACTVS 3.341 "C[CH]1O[CH](C[CH](N)[CH]1O)O[CH]2C[C](O)(Cc3c(O)c4C(=O)c5ccccc5C(=O)c4c(O)c23)C(C)=O" DM5 SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C[C@H]1[C@H]([C@H](C[C@@H](O1)O[C@H]2C[C@@](Cc3c2c(c4c(c3O)C(=O)c5ccccc5C4=O)O)(C(=O)C)O)N)O" DM5 SMILES "OpenEye OEToolkits" 1.5.0 "CC1C(C(CC(O1)OC2CC(Cc3c2c(c4c(c3O)C(=O)c5ccccc5C4=O)O)(C(=O)C)O)N)O" DM5 InChI InChI 1.03 "InChI=1S/C26H27NO9/c1-10-21(29)15(27)7-17(35-10)36-16-9-26(34,11(2)28)8-14-18(16)25(33)20-19(24(14)32)22(30)12-5-3-4-6-13(12)23(20)31/h3-6,10,15-17,21,29,32-34H,7-9,27H2,1-2H3/t10-,15-,16-,17-,21+,26-/m0/s1" DM5 InChIKey InChI 1.03 XDXDZDZNSLXDNA-TZNDIEGXSA-N # # loop_ _pdbx_chem_comp_identifier.comp_id _pdbx_chem_comp_identifier.type _pdbx_chem_comp_identifier.program _pdbx_chem_comp_identifier.program_version _pdbx_chem_comp_identifier.identifier DM5 "SYSTEMATIC NAME" ACDLabs 10.04 "(1S,3S)-3-acetyl-3,5,12-trihydroxy-6,11-dioxo-1,2,3,4,6,11-hexahydrotetracen-1-yl 3-amino-2,3,6-trideoxy-alpha-L-lyxo-hexopyranoside" DM5 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "(7S,9S)-7-[(2R,4S,5S,6S)-4-amino-5-hydroxy-6-methyl-oxan-2-yl]oxy-9-ethanoyl-6,9,11-trihydroxy-8,10-dihydro-7H-tetracene-5,12-dione" # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site DM5 "Create component" 1999-07-08 RCSB DM5 "Modify descriptor" 2011-06-04 RCSB DM5 "Modify synonyms" 2020-06-05 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id DM5 _pdbx_chem_comp_synonyms.name 4-DEMETHOXY-DAUNORUBICIN _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##