data_ZOD # _chem_comp.id ZOD _chem_comp.name "[(2R,3R,4R,5R)-5-[[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxymethyl]-2,4-bis(oxidanyl)oxolan-3-yl] ethanoate" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C17 H25 N5 O15 P2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2015-07-07 _chem_comp.pdbx_modified_date 2015-10-30 _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 601.352 _chem_comp.one_letter_code ? _chem_comp.three_letter_code ZOD _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 5CB5 _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 ZOD C01 C1 C 0 1 N N N 3.122 -65.885 -55.531 9.821 4.334 -0.056 C01 ZOD 1 ZOD C02 C2 C 0 1 N N N 2.054 -64.934 -55.154 9.159 3.097 0.494 C02 ZOD 2 ZOD O03 O1 O 0 1 N N N 2.141 -63.780 -54.711 9.526 2.632 1.547 O03 ZOD 3 ZOD O04 O2 O 0 1 N N N 0.774 -65.463 -55.239 8.161 2.511 -0.187 O04 ZOD 4 ZOD C05 C3 C 0 1 N N R -0.017 -65.009 -56.309 7.570 1.323 0.403 C05 ZOD 5 ZOD C06 C4 C 0 1 N N R 0.102 -63.570 -56.705 6.337 1.698 1.255 C06 ZOD 6 ZOD O07 O3 O 0 1 N N N -0.635 -62.746 -55.815 6.692 1.766 2.638 O07 ZOD 7 ZOD O08 O4 O 0 1 N N N -0.574 -63.583 -57.984 5.394 0.628 1.031 O08 ZOD 8 ZOD C09 C5 C 0 1 N N R -0.463 -64.921 -58.561 5.489 0.326 -0.379 C09 ZOD 9 ZOD C10 C6 C 0 1 N N N -1.882 -65.527 -58.725 4.953 -1.079 -0.660 C10 ZOD 10 ZOD O1B O5 O 0 1 N N N -2.511 -64.855 -59.835 3.548 -1.114 -0.400 O1B ZOD 11 ZOD PB P1 P 0 1 N N N -4.098 -64.616 -59.735 2.654 -2.439 -0.591 PB ZOD 12 ZOD O2B O6 O 0 1 N N N -4.511 -63.720 -60.848 2.822 -2.953 -1.969 O2B ZOD 13 ZOD O3B O7 O 0 1 N N N -4.902 -65.885 -59.818 3.127 -3.562 0.461 O3B ZOD 14 ZOD O3A O8 O 0 1 N N N -4.518 -63.880 -58.419 1.105 -2.083 -0.336 O3A ZOD 15 ZOD PA P2 P 0 1 N N N -4.247 -62.386 -57.828 -0.283 -2.835 -0.653 PA ZOD 16 ZOD O2A O9 O 0 1 N N N -3.969 -62.501 -56.267 -0.609 -2.719 -2.225 O2A ZOD 17 ZOD O1A O10 O 0 1 N N N -3.081 -61.705 -58.556 -0.168 -4.261 -0.277 O1A ZOD 18 ZOD "O5'" O11 O 0 1 N N N -5.589 -61.526 -58.121 -1.469 -2.151 0.193 "O5'" ZOD 19 ZOD "C5'" C7 C 0 1 N N N -6.711 -62.252 -58.567 -2.806 -2.657 0.209 "C5'" ZOD 20 ZOD "C4'" C8 C 0 1 N N R -7.979 -61.538 -58.100 -3.674 -1.775 1.108 "C4'" ZOD 21 ZOD "O4'" O12 O 0 1 N N N -7.973 -61.208 -56.683 -3.807 -0.467 0.528 "O4'" ZOD 22 ZOD "C1'" C9 C 0 1 N N R -8.606 -59.915 -56.623 -5.130 0.009 0.858 "C1'" ZOD 23 ZOD N9 N1 N 0 1 Y N N -8.275 -59.494 -55.298 -5.548 1.060 -0.073 N9 ZOD 24 ZOD C8 C10 C 0 1 Y N N -7.169 -58.896 -54.796 -5.075 1.252 -1.337 C8 ZOD 25 ZOD N7 N2 N 0 1 Y N N -7.344 -58.704 -53.466 -5.665 2.277 -1.881 N7 ZOD 26 ZOD C5 C11 C 0 1 Y N N -8.609 -59.198 -53.118 -6.551 2.806 -1.003 C5 ZOD 27 ZOD C6 C12 C 0 1 Y N N -9.379 -59.293 -51.893 -7.447 3.888 -1.034 C6 ZOD 28 ZOD N6 N3 N 0 1 N N N -8.821 -58.797 -50.628 -7.555 4.686 -2.159 N6 ZOD 29 ZOD N1 N4 N 0 1 Y N N -10.629 -59.825 -51.924 -8.189 4.126 0.043 N1 ZOD 30 ZOD C2 C13 C 0 1 Y N N -11.136 -60.284 -53.077 -8.093 3.370 1.121 C2 ZOD 31 ZOD N3 N5 N 0 1 Y N N -10.462 -60.240 -54.269 -7.268 2.347 1.195 N3 ZOD 32 ZOD C4 C14 C 0 1 Y N N -9.191 -59.689 -54.272 -6.491 2.027 0.165 C4 ZOD 33 ZOD "C2'" C15 C 0 1 N N R -8.215 -59.156 -57.859 -6.018 -1.251 0.694 "C2'" ZOD 34 ZOD "O2'" O13 O 0 1 N N N -9.261 -58.280 -58.295 -7.199 -1.150 1.492 "O2'" ZOD 35 ZOD "C3'" C16 C 0 1 N N S -8.011 -60.231 -58.864 -5.090 -2.373 1.219 "C3'" ZOD 36 ZOD "O3'" O14 O 0 1 N N N -9.025 -60.323 -59.810 -5.398 -2.681 2.580 "O3'" ZOD 37 ZOD C38 C17 C 0 1 N N R 0.323 -65.730 -57.567 7.002 0.398 -0.697 C38 ZOD 38 ZOD O39 O15 O 0 1 N N N 1.690 -65.727 -57.942 7.215 0.969 -1.990 O39 ZOD 39 ZOD H1 H1 H 0 1 N N N 4.104 -65.420 -55.362 10.602 4.663 0.630 H1 ZOD 40 ZOD H10 H2 H 0 1 N N N 3.037 -66.794 -54.917 10.262 4.109 -1.027 H10 ZOD 41 ZOD H3 H3 H 0 1 N N N 3.019 -66.149 -56.594 9.079 5.124 -0.167 H3 ZOD 42 ZOD H4 H4 H 0 1 N N N -1.075 -65.208 -56.081 8.305 0.791 1.007 H4 ZOD 43 ZOD H5 H5 H 0 1 N N N 1.155 -63.263 -56.794 5.921 2.649 0.923 H5 ZOD 44 ZOD H6 H6 H 0 1 N N N -0.203 -62.727 -54.969 5.956 1.998 3.221 H6 ZOD 45 ZOD H7 H7 H 0 1 N N N 0.050 -64.896 -59.534 4.942 1.066 -0.963 H7 ZOD 46 ZOD H11 H8 H 0 1 N N N -2.468 -65.367 -57.808 5.136 -1.335 -1.704 H11 ZOD 47 ZOD H9 H9 H 0 1 N N N -1.809 -66.605 -58.930 5.460 -1.797 -0.015 H9 ZOD 48 ZOD HOB3 H10 H 0 0 N N N -5.495 -65.837 -60.559 3.045 -3.293 1.387 HOB3 ZOD 49 ZOD HOA2 H11 H 0 0 N N N -3.121 -62.122 -56.067 -0.698 -1.810 -2.543 HOA2 ZOD 50 ZOD "H5'1" H12 H 0 0 N N N -6.702 -62.308 -59.666 -3.208 -2.652 -0.803 "H5'1" ZOD 51 ZOD "H5'2" H13 H 0 0 N N N -6.684 -63.269 -58.148 -2.803 -3.677 0.595 "H5'2" ZOD 52 ZOD "H4'" H14 H 0 1 N N N -8.861 -62.143 -58.356 -3.224 -1.697 2.098 "H4'" ZOD 53 ZOD "H1'" H15 H 0 1 N N N -9.694 -60.070 -56.669 -5.162 0.372 1.885 "H1'" ZOD 54 ZOD H8 H16 H 0 1 N N N -6.292 -58.618 -55.362 -4.322 0.644 -1.816 H8 ZOD 55 ZOD HN61 H17 H 0 0 N N N -9.489 -58.926 -49.895 -7.008 4.501 -2.939 HN61 ZOD 56 ZOD HN62 H18 H 0 0 N N N -7.986 -59.303 -50.411 -8.177 5.430 -2.168 HN62 ZOD 57 ZOD H2 H19 H 0 1 N N N -12.128 -60.711 -53.066 -8.715 3.599 1.974 H2 ZOD 58 ZOD "H2'" H20 H 0 1 N N N -7.278 -58.606 -57.688 -6.272 -1.414 -0.354 "H2'" ZOD 59 ZOD "HO2'" H21 H 0 0 N N N -9.389 -57.594 -57.651 -7.787 -1.914 1.423 "HO2'" ZOD 60 ZOD "H3'" H22 H 0 1 N N N -7.038 -60.085 -59.355 -5.178 -3.263 0.596 "H3'" ZOD 61 ZOD "HO3'" H23 H 0 0 N N N -9.069 -59.515 -60.307 -6.278 -3.061 2.708 "HO3'" ZOD 62 ZOD H24 H24 H 0 1 N N N -0.072 -66.756 -57.529 7.452 -0.593 -0.637 H24 ZOD 63 ZOD H25 H25 H 0 1 N N N 2.191 -66.237 -57.317 8.146 1.038 -2.241 H25 ZOD 64 # 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 ZOD O2B PB DOUB N N 1 ZOD O1B PB SING N N 2 ZOD O1B C10 SING N N 3 ZOD O3B PB SING N N 4 ZOD "O3'" "C3'" SING N N 5 ZOD PB O3A SING N N 6 ZOD "C3'" "C4'" SING N N 7 ZOD "C3'" "C2'" SING N N 8 ZOD C10 C09 SING N N 9 ZOD "C5'" "O5'" SING N N 10 ZOD "C5'" "C4'" SING N N 11 ZOD C09 O08 SING N N 12 ZOD C09 C38 SING N N 13 ZOD O1A PA DOUB N N 14 ZOD O3A PA SING N N 15 ZOD "O2'" "C2'" SING N N 16 ZOD "O5'" PA SING N N 17 ZOD "C4'" "O4'" SING N N 18 ZOD O08 C06 SING N N 19 ZOD O39 C38 SING N N 20 ZOD "C2'" "C1'" SING N N 21 ZOD PA O2A SING N N 22 ZOD C38 C05 SING N N 23 ZOD C06 C05 SING N N 24 ZOD C06 O07 SING N N 25 ZOD "O4'" "C1'" SING N N 26 ZOD "C1'" N9 SING N N 27 ZOD C05 O04 SING N N 28 ZOD C01 C02 SING N N 29 ZOD N9 C8 SING Y N 30 ZOD N9 C4 SING Y N 31 ZOD O04 C02 SING N N 32 ZOD C02 O03 DOUB N N 33 ZOD C8 N7 DOUB Y N 34 ZOD C4 N3 SING Y N 35 ZOD C4 C5 DOUB Y N 36 ZOD N3 C2 DOUB Y N 37 ZOD N7 C5 SING Y N 38 ZOD C5 C6 SING Y N 39 ZOD C2 N1 SING Y N 40 ZOD N1 C6 DOUB Y N 41 ZOD C6 N6 SING N N 42 ZOD C01 H1 SING N N 43 ZOD C01 H10 SING N N 44 ZOD C01 H3 SING N N 45 ZOD C05 H4 SING N N 46 ZOD C06 H5 SING N N 47 ZOD O07 H6 SING N N 48 ZOD C09 H7 SING N N 49 ZOD C10 H11 SING N N 50 ZOD C10 H9 SING N N 51 ZOD O3B HOB3 SING N N 52 ZOD O2A HOA2 SING N N 53 ZOD "C5'" "H5'1" SING N N 54 ZOD "C5'" "H5'2" SING N N 55 ZOD "C4'" "H4'" SING N N 56 ZOD "C1'" "H1'" SING N N 57 ZOD C8 H8 SING N N 58 ZOD N6 HN61 SING N N 59 ZOD N6 HN62 SING N N 60 ZOD C2 H2 SING N N 61 ZOD "C2'" "H2'" SING N N 62 ZOD "O2'" "HO2'" SING N N 63 ZOD "C3'" "H3'" SING N N 64 ZOD "O3'" "HO3'" SING N N 65 ZOD C38 H24 SING N N 66 ZOD O39 H25 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 ZOD SMILES ACDLabs 12.01 "CC(=O)OC1C(O)OC(C1O)COP(OP(O)(=O)OCC4OC(n2cnc3c(N)ncnc23)C(O)C4O)(=O)O" ZOD InChI InChI 1.03 "InChI=1S/C17H25N5O15P2/c1-6(23)34-13-11(25)8(36-17(13)27)3-33-39(30,31)37-38(28,29)32-2-7-10(24)12(26)16(35-7)22-5-21-9-14(18)19-4-20-15(9)22/h4-5,7-8,10-13,16-17,24-27H,2-3H2,1H3,(H,28,29)(H,30,31)(H2,18,19,20)/t7-,8-,10-,11-,12-,13-,16-,17-/m1/s1" ZOD InChIKey InChI 1.03 BFNOPXRXIQJDHO-QJWJOKBXSA-N ZOD SMILES_CANONICAL CACTVS 3.385 "CC(=O)O[C@H]1[C@H](O)O[C@H](CO[P](O)(=O)O[P](O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)n3cnc4c(N)ncnc34)[C@H]1O" ZOD SMILES CACTVS 3.385 "CC(=O)O[CH]1[CH](O)O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]2O[CH]([CH](O)[CH]2O)n3cnc4c(N)ncnc34)[CH]1O" ZOD SMILES_CANONICAL "OpenEye OEToolkits" 1.9.2 "CC(=O)O[C@@H]1[C@@H]([C@H](O[C@H]1O)COP(=O)(O)OP(=O)(O)OC[C@@H]2[C@H]([C@H]([C@@H](O2)n3cnc4c3ncnc4N)O)O)O" ZOD SMILES "OpenEye OEToolkits" 1.9.2 "CC(=O)OC1C(C(OC1O)COP(=O)(O)OP(=O)(O)OCC2C(C(C(O2)n3cnc4c3ncnc4N)O)O)O" # 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 ZOD "SYSTEMATIC NAME" ACDLabs 12.01 "(2R,3R,4R,5R)-5-({[(R)-{[(R)-{[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}methyl)-2,4-dihydroxytetrahydrofuran-3-yl acetate (non-preferred name)" ZOD "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.9.2 "[(2R,3R,4R,5R)-5-[[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxymethyl]-2,4-bis(oxidanyl)oxolan-3-yl] ethanoate" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site ZOD "Create component" 2015-07-07 PDBJ ZOD "Initial release" 2015-11-04 RCSB #