data_DM3 # _chem_comp.id DM3 _chem_comp.name 6-DEOXYDAUNOMYCIN _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAD _chem_comp.formula "C27 H29 N O9" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 1999-07-08 _chem_comp.pdbx_modified_date 2011-06-04 _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 511.520 _chem_comp.one_letter_code ? _chem_comp.three_letter_code DM3 _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 1D14 _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 DM3 C1 C1 C 0 1 Y N N 9.002 21.100 33.532 -0.954 -0.438 6.081 C1 DM3 1 DM3 C2 C2 C 0 1 Y N N 7.680 20.629 33.252 -0.020 0.017 6.998 C2 DM3 2 DM3 C3 C3 C 0 1 Y N N 7.394 19.282 33.174 1.221 0.446 6.581 C3 DM3 3 DM3 C4 C4 C 0 1 Y N N 8.420 18.382 33.345 1.556 0.427 5.229 C4 DM3 4 DM3 O4 O4 O 0 1 N N N 8.168 17.010 33.262 2.779 0.849 4.824 O4 DM3 5 DM3 C5 C5 C 0 1 Y N N 9.732 18.817 33.650 0.623 -0.023 4.293 C5 DM3 6 DM3 C6 C6 C 0 1 N N N 10.789 17.952 33.814 0.957 -0.057 2.856 C6 DM3 7 DM3 O6 O6 O 0 1 N N N 10.476 16.610 33.732 2.109 0.072 2.488 O6 DM3 8 DM3 C7 C7 C 0 1 Y N N 12.086 18.417 34.093 -0.124 -0.246 1.870 C7 DM3 9 DM3 C8 C8 C 0 1 Y N N 13.168 17.576 34.266 0.091 0.003 0.516 C8 DM3 10 DM3 O8 O8 O 0 1 N N N 13.135 16.191 34.194 1.308 0.423 0.093 O8 DM3 11 DM3 C9 C9 C 0 1 Y N N 14.425 18.170 34.564 -0.944 -0.177 -0.407 C9 DM3 12 DM3 C10 C10 C 0 1 N N S 15.523 17.148 34.725 -0.642 0.119 -1.853 C10 DM3 13 DM3 O10 O10 O 0 1 N N N 15.669 16.622 33.324 0.647 -0.400 -2.181 O10 DM3 14 DM3 C11 C11 C 0 1 N N N 16.792 17.814 35.233 -1.688 -0.519 -2.764 C11 DM3 15 DM3 C12 C12 C 0 1 N N S 17.075 19.194 34.766 -3.079 -0.118 -2.257 C12 DM3 16 DM3 O12 O12 O 0 1 N N N 17.326 19.016 33.273 -4.070 -0.511 -3.208 O12 DM3 17 DM3 C13 C13 C 0 1 N N N 18.423 19.836 35.155 -3.135 1.373 -2.051 C13 DM3 18 DM3 O13 O13 O 0 1 N N N 18.298 20.856 36.045 -2.914 1.841 -0.960 O13 DM3 19 DM3 C14 C14 C 0 1 N N N 19.687 19.455 34.442 -3.467 2.281 -3.208 C14 DM3 20 DM3 C15 C15 C 0 1 N N N 15.960 20.185 34.958 -3.329 -0.830 -0.929 C15 DM3 21 DM3 C16 C16 C 0 1 Y N N 14.649 19.518 34.659 -2.179 -0.607 0.018 C16 DM3 22 DM3 C17 C17 C 0 1 Y N N 13.571 20.381 34.452 -2.404 -0.860 1.369 C17 DM3 23 DM3 C18 C18 C 0 1 Y N N 12.340 19.745 34.167 -1.392 -0.683 2.300 C18 DM3 24 DM3 C19 C19 C 0 1 N N N 11.275 20.644 33.981 -1.627 -0.947 3.736 C19 DM3 25 DM3 O19 O19 O 0 1 N N N 11.439 21.952 34.014 -2.617 -1.553 4.096 O19 DM3 26 DM3 C20 C20 C 0 1 Y N N 9.997 20.141 33.720 -0.641 -0.465 4.727 C20 DM3 27 DM3 C21 C21 C 0 1 N N N 6.809 16.663 32.939 3.489 1.247 5.999 C21 DM3 28 DM3 "C1'" C1* C 0 1 N N R 16.091 15.299 33.003 1.386 0.669 -2.773 "C1'" DM3 29 DM3 "C2'" C2* C 0 1 N N N 15.820 14.997 31.529 2.863 0.278 -2.865 "C2'" DM3 30 DM3 "C3'" C3* C 0 1 N N S 16.874 15.676 30.696 2.990 -0.996 -3.706 "C3'" DM3 31 DM3 "N3'" N3* N 0 1 N N N 16.658 15.042 29.333 4.410 -1.299 -3.930 "N3'" DM3 32 DM3 "C4'" C4* C 0 1 N N S 18.372 15.415 31.105 2.290 -0.769 -5.050 "C4'" DM3 33 DM3 "O4'" O4* O 0 1 N N N 18.616 14.002 30.939 2.995 0.225 -5.794 "O4'" DM3 34 DM3 "C5'" C5* C 0 1 N N S 18.532 15.801 32.566 0.856 -0.299 -4.793 "C5'" DM3 35 DM3 "O5'" O5* O 0 1 N N N 17.478 15.017 33.332 0.875 0.933 -4.078 "O5'" DM3 36 DM3 "C6'" C6* C 0 1 N N N 19.918 15.575 33.133 0.138 -0.100 -6.129 "C6'" DM3 37 DM3 H1 H1 H 0 1 N N N 9.247 22.173 33.601 -1.924 -0.772 6.417 H1 DM3 38 DM3 H2 H2 H 0 1 N N N 6.846 21.333 33.089 -0.268 0.037 8.049 H2 DM3 39 DM3 H3 H3 H 0 1 N N N 6.366 18.931 32.979 1.939 0.798 7.307 H3 DM3 40 DM3 HO8 HO8 H 0 1 N N N 13.879 15.612 34.313 1.282 1.390 0.080 HO8 DM3 41 DM3 H10 H10 H 0 1 N N N 15.308 16.342 35.465 -0.644 1.198 -2.006 H10 DM3 42 DM3 H111 1H11 H 0 0 N N N 16.798 17.793 36.347 -1.586 -1.604 -2.736 H111 DM3 43 DM3 H112 2H11 H 0 0 N N N 17.667 17.161 35.006 -1.553 -0.163 -3.785 H112 DM3 44 DM3 HO12 2HO1 H 0 0 N N N 17.507 19.899 32.974 -4.927 -0.256 -2.840 HO12 DM3 45 DM3 H141 1H14 H 0 0 N N N 20.661 19.918 34.723 -3.460 3.317 -2.870 H141 DM3 46 DM3 H142 2H14 H 0 0 N N N 19.799 18.347 34.500 -2.725 2.151 -3.996 H142 DM3 47 DM3 H143 3H14 H 0 0 N N N 19.530 19.609 33.349 -4.455 2.031 -3.594 H143 DM3 48 DM3 H151 1H15 H 0 0 N N N 15.976 20.649 35.971 -3.444 -1.899 -1.111 H151 DM3 49 DM3 H152 2H15 H 0 0 N N N 16.109 21.112 34.356 -4.244 -0.443 -0.481 H152 DM3 50 DM3 H17 H17 H 0 1 N N N 13.682 21.476 34.509 -3.377 -1.197 1.695 H17 DM3 51 DM3 H211 1H21 H 0 0 N N N 6.607 15.568 32.872 4.484 1.597 5.721 H211 DM3 52 DM3 H212 2H21 H 0 0 N N N 6.106 17.141 33.660 2.947 2.052 6.496 H212 DM3 53 DM3 H213 3H21 H 0 0 N N N 6.494 17.170 31.997 3.578 0.397 6.675 H213 DM3 54 DM3 "H1'" H1* H 0 1 N N N 15.484 14.622 33.649 1.286 1.563 -2.157 "H1'" DM3 55 DM3 "H2'1" 1H2* H 0 0 N N N 15.752 13.903 31.322 3.424 1.084 -3.337 "H2'1" DM3 56 DM3 "H2'2" 2H2* H 0 0 N N N 14.785 15.276 31.219 3.255 0.096 -1.864 "H2'2" DM3 57 DM3 "H3'" H3* H 0 1 N N N 16.757 16.781 30.786 2.517 -1.828 -3.183 "H3'" DM3 58 DM3 "HN'1" 1HN* H 0 0 N N N 17.372 15.502 28.768 4.826 -1.427 -3.021 "HN'1" DM3 59 DM3 "HN'2" 2HN* H 0 0 N N N 15.707 15.113 28.969 4.445 -2.194 -4.394 "HN'2" DM3 60 DM3 "H4'" H4* H 0 1 N N N 19.086 16.005 30.485 2.271 -1.702 -5.614 "H4'" DM3 61 DM3 "HO4'" *HO4 H 0 0 N N N 19.519 13.844 31.185 2.522 0.337 -6.630 "HO4'" DM3 62 DM3 "H5'" H5* H 0 1 N N N 18.392 16.902 32.665 0.328 -1.050 -4.206 "H5'" DM3 63 DM3 "H6'1" 1H6* H 0 0 N N N 20.035 15.858 34.205 -0.882 0.234 -5.947 "H6'1" DM3 64 DM3 "H6'2" 2H6* H 0 0 N N N 20.232 14.516 32.976 0.667 0.649 -6.718 "H6'2" DM3 65 DM3 "H6'3" 3H6* H 0 0 N N N 20.680 16.097 32.509 0.119 -1.043 -6.675 "H6'3" DM3 66 # 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 DM3 C1 C2 DOUB Y N 1 DM3 C1 C20 SING Y N 2 DM3 C1 H1 SING N N 3 DM3 C2 C3 SING Y N 4 DM3 C2 H2 SING N N 5 DM3 C3 C4 DOUB Y N 6 DM3 C3 H3 SING N N 7 DM3 C4 O4 SING N N 8 DM3 C4 C5 SING Y N 9 DM3 O4 C21 SING N N 10 DM3 C5 C6 SING N N 11 DM3 C5 C20 DOUB Y N 12 DM3 C6 O6 DOUB N N 13 DM3 C6 C7 SING N N 14 DM3 C7 C8 DOUB Y N 15 DM3 C7 C18 SING Y N 16 DM3 C8 O8 SING N N 17 DM3 C8 C9 SING Y N 18 DM3 O8 HO8 SING N N 19 DM3 C9 C10 SING N N 20 DM3 C9 C16 DOUB Y N 21 DM3 C10 O10 SING N N 22 DM3 C10 C11 SING N N 23 DM3 C10 H10 SING N N 24 DM3 O10 "C1'" SING N N 25 DM3 C11 C12 SING N N 26 DM3 C11 H111 SING N N 27 DM3 C11 H112 SING N N 28 DM3 C12 O12 SING N N 29 DM3 C12 C13 SING N N 30 DM3 C12 C15 SING N N 31 DM3 O12 HO12 SING N N 32 DM3 C13 O13 DOUB N N 33 DM3 C13 C14 SING N N 34 DM3 C14 H141 SING N N 35 DM3 C14 H142 SING N N 36 DM3 C14 H143 SING N N 37 DM3 C15 C16 SING N N 38 DM3 C15 H151 SING N N 39 DM3 C15 H152 SING N N 40 DM3 C16 C17 SING Y N 41 DM3 C17 C18 DOUB Y N 42 DM3 C17 H17 SING N N 43 DM3 C18 C19 SING N N 44 DM3 C19 O19 DOUB N N 45 DM3 C19 C20 SING N N 46 DM3 C21 H211 SING N N 47 DM3 C21 H212 SING N N 48 DM3 C21 H213 SING N N 49 DM3 "C1'" "C2'" SING N N 50 DM3 "C1'" "O5'" SING N N 51 DM3 "C1'" "H1'" SING N N 52 DM3 "C2'" "C3'" SING N N 53 DM3 "C2'" "H2'1" SING N N 54 DM3 "C2'" "H2'2" SING N N 55 DM3 "C3'" "N3'" SING N N 56 DM3 "C3'" "C4'" SING N N 57 DM3 "C3'" "H3'" SING N N 58 DM3 "N3'" "HN'1" SING N N 59 DM3 "N3'" "HN'2" SING N N 60 DM3 "C4'" "O4'" SING N N 61 DM3 "C4'" "C5'" SING N N 62 DM3 "C4'" "H4'" SING N N 63 DM3 "O4'" "HO4'" SING N N 64 DM3 "C5'" "O5'" SING N N 65 DM3 "C5'" "C6'" SING N N 66 DM3 "C5'" "H5'" SING N N 67 DM3 "C6'" "H6'1" SING N N 68 DM3 "C6'" "H6'2" SING N N 69 DM3 "C6'" "H6'3" SING N N 70 # 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 DM3 SMILES ACDLabs 10.04 "O=C2c1cc5c(c(O)c1C(=O)c3c2cccc3OC)C(OC4OC(C(O)C(N)C4)C)CC(O)(C(=O)C)C5" DM3 SMILES_CANONICAL CACTVS 3.341 "COc1cccc2C(=O)c3cc4C[C@](O)(C[C@H](O[C@H]5C[C@H](N)[C@H](O)[C@H](C)O5)c4c(O)c3C(=O)c12)C(C)=O" DM3 SMILES CACTVS 3.341 "COc1cccc2C(=O)c3cc4C[C](O)(C[CH](O[CH]5C[CH](N)[CH](O)[CH](C)O5)c4c(O)c3C(=O)c12)C(C)=O" DM3 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(c3)C(=O)c5cccc(c5C4=O)OC)O)(C(=O)C)O)N)O" DM3 SMILES "OpenEye OEToolkits" 1.5.0 "CC1C(C(CC(O1)OC2CC(Cc3c2c(c4c(c3)C(=O)c5cccc(c5C4=O)OC)O)(C(=O)C)O)N)O" DM3 InChI InChI 1.03 "InChI=1S/C27H29NO9/c1-11-23(30)16(28)8-19(36-11)37-18-10-27(34,12(2)29)9-13-7-15-22(25(32)20(13)18)26(33)21-14(24(15)31)5-4-6-17(21)35-3/h4-7,11,16,18-19,23,30,32,34H,8-10,28H2,1-3H3/t11-,16-,18-,19-,23+,27-/m0/s1" DM3 InChIKey InChI 1.03 ZCLQMQOBRBUQOR-GRRPPOEGSA-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 DM3 "SYSTEMATIC NAME" ACDLabs 10.04 "(1S,3S)-3-acetyl-3,12-dihydroxy-10-methoxy-6,11-dioxo-1,2,3,4,6,11-hexahydrotetracen-1-yl 3-amino-2,3,6-trideoxy-alpha-L-lyxo-hexopyranoside" DM3 "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-dihydroxy-4-methoxy-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 DM3 "Create component" 1999-07-08 RCSB DM3 "Modify descriptor" 2011-06-04 RCSB #