data_3ZO # _chem_comp.id 3ZO _chem_comp.name "2'-DEOXY-XANTHOSINE-5'-MONOPHOSPHATE" _chem_comp.type "DNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C10 H13 N4 O8 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "2'-deoxy-5'-2,3-dihydroxanthylic acid" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2014-12-24 _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 348.206 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 3ZO _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 2MWZ _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 3ZO P P P 0 1 N N N 22.814 28.577 18.277 5.086 0.776 0.350 P 3ZO 1 3ZO "C5'" "C5'" C 0 1 N N N 22.563 27.049 20.438 3.037 -0.716 -0.495 "C5'" 3ZO 2 3ZO "O5'" "O5'" O 0 1 N N N 22.395 28.332 19.817 3.658 0.056 0.534 "O5'" 3ZO 3 3ZO "C4'" "C4'" C 0 1 N N R 22.343 27.120 21.952 1.697 -1.255 0.009 "C4'" 3ZO 4 3ZO "O4'" "O4'" O 0 1 N N N 23.303 28.012 22.537 0.746 -0.178 0.158 "O4'" 3ZO 5 3ZO "C3'" "C3'" C 0 1 N N S 20.951 27.627 22.366 1.066 -2.195 -1.042 "C3'" 3ZO 6 3ZO "O3'" "O3'" O 0 1 N N N 20.445 26.821 23.439 1.326 -3.561 -0.712 "O3'" 3ZO 7 3ZO "C2'" "C2'" C 0 1 N N N 21.219 29.035 22.876 -0.448 -1.896 -0.952 "C2'" 3ZO 8 3ZO "C1'" "C1'" C 0 1 N N R 22.606 28.852 23.454 -0.552 -0.811 0.142 "C1'" 3ZO 9 3ZO N1 N1 N 0 1 N N N 25.504 31.539 26.607 -5.634 0.426 0.444 N1 3ZO 10 3ZO C2 C2 C 0 1 N N N 24.911 30.314 26.780 -5.004 -0.656 0.931 C2 3ZO 11 3ZO O2 O2 O 0 1 N N N 25.111 29.768 27.854 -5.652 -1.493 1.530 O2 3ZO 12 3ZO N3 N3 N 0 1 N N N 24.171 29.714 25.859 -3.681 -0.846 0.778 N3 3ZO 13 3ZO C4 C4 C 0 1 Y N N 24.073 30.450 24.735 -2.910 0.074 0.107 C4 3ZO 14 3ZO C5 C5 C 0 1 Y N N 24.632 31.674 24.473 -3.514 1.211 -0.417 C5 3ZO 15 3ZO C6 C6 C 0 1 N N N 25.421 32.308 25.466 -4.957 1.378 -0.233 C6 3ZO 16 3ZO O6 O6 O 0 1 N N N 25.987 33.391 25.418 -5.531 2.356 -0.674 O6 3ZO 17 3ZO N7 N7 N 0 1 Y N N 24.294 32.097 23.195 -2.546 1.942 -1.020 N7 3ZO 18 3ZO C8 C8 C 0 1 Y N N 23.554 31.126 22.733 -1.407 1.325 -0.896 C8 3ZO 19 3ZO N9 N9 N 0 1 Y N N 23.377 30.095 23.616 -1.590 0.163 -0.204 N9 3ZO 20 3ZO OP1 OP1 O 0 1 N N N 22.475 27.360 17.503 6.094 -0.226 -0.065 OP1 3ZO 21 3ZO OP2 OP2 O 0 1 N N N 22.272 29.890 17.858 4.969 1.919 -0.778 OP2 3ZO 22 3ZO OP3 OP3 O 0 1 N Y N 24.421 28.692 18.352 5.535 1.443 1.745 OP3 3ZO 23 3ZO "H5''" "H5''" H 0 0 N N N 21.837 26.345 20.005 2.870 -0.088 -1.370 "H5''" 3ZO 24 3ZO "H5'" "H5'" H 0 1 N N N 23.584 26.689 20.243 3.685 -1.550 -0.765 "H5'" 3ZO 25 3ZO "H4'" "H4'" H 0 1 N N N 22.478 26.111 22.368 1.831 -1.779 0.955 "H4'" 3ZO 26 3ZO "H3'" "H3'" H 0 1 N N N 20.271 27.645 21.502 1.442 -1.963 -2.038 "H3'" 3ZO 27 3ZO H2 H2 H 0 1 N N N 19.585 27.135 23.694 0.952 -4.195 -1.339 H2 3ZO 28 3ZO "H2'" "H2'" H 0 1 N N N 21.212 29.772 22.060 -0.819 -1.516 -1.904 "H2'" 3ZO 29 3ZO "H2''" "H2''" H 0 0 N N N 20.493 29.334 23.646 -0.997 -2.790 -0.656 "H2''" 3ZO 30 3ZO "H1'" "H1'" H 0 1 N N N 22.518 28.350 24.429 -0.764 -1.266 1.109 "H1'" 3ZO 31 3ZO H1 H1 H 0 1 N N N 26.039 31.903 27.369 -6.590 0.522 0.577 H1 3ZO 32 3ZO H3 H3 H 0 1 N N N 23.737 28.822 25.983 -3.266 -1.642 1.146 H3 3ZO 33 3ZO H8 H8 H 0 1 N N N 23.121 31.135 21.744 -0.462 1.678 -1.281 H8 3ZO 34 3ZO H4 H4 H 0 1 N N N 21.732 29.778 17.084 4.326 2.610 -0.572 H4 3ZO 35 3ZO HOP3 HOP3 H 0 0 N N N 24.813 27.962 17.888 6.389 1.895 1.708 HOP3 3ZO 36 # # 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 3ZO OP1 P DOUB N N 1 3ZO OP2 P SING N N 2 3ZO P "O5'" SING N N 3 3ZO "O5'" "C5'" SING N N 4 3ZO "C5'" "C4'" SING N N 5 3ZO "C4'" "C3'" SING N N 6 3ZO "C4'" "O4'" SING N N 7 3ZO "C3'" "C2'" SING N N 8 3ZO "C3'" "O3'" SING N N 9 3ZO "O4'" "C1'" SING N N 10 3ZO C8 N7 DOUB Y N 11 3ZO C8 N9 SING Y N 12 3ZO "C2'" "C1'" SING N N 13 3ZO N7 C5 SING Y N 14 3ZO "C1'" N9 SING N N 15 3ZO N9 C4 SING Y N 16 3ZO C5 C4 DOUB Y N 17 3ZO C5 C6 SING N N 18 3ZO C4 N3 SING N N 19 3ZO O6 C6 DOUB N N 20 3ZO C6 N1 SING N N 21 3ZO N3 C2 SING N N 22 3ZO N1 C2 SING N N 23 3ZO C2 O2 DOUB N N 24 3ZO P OP3 SING N N 25 3ZO "C5'" "H5''" SING N N 26 3ZO "C5'" "H5'" SING N N 27 3ZO "C4'" "H4'" SING N N 28 3ZO "C3'" "H3'" SING N N 29 3ZO "O3'" H2 SING N N 30 3ZO "C2'" "H2'" SING N N 31 3ZO "C2'" "H2''" SING N N 32 3ZO "C1'" "H1'" SING N N 33 3ZO N1 H1 SING N N 34 3ZO N3 H3 SING N N 35 3ZO C8 H8 SING N N 36 3ZO OP2 H4 SING N N 37 3ZO OP3 HOP3 SING N N 38 # # 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 3ZO SMILES ACDLabs 12.01 "O=P(O)(O)OCC3OC(n1cnc2c1NC(=O)NC2=O)CC3O" 3ZO InChI InChI 1.03 "InChI=1S/C10H13N4O8P/c15-4-1-6(22-5(4)2-21-23(18,19)20)14-3-11-7-8(14)12-10(17)13-9(7)16/h3-6,15H,1-2H2,(H2,18,19,20)(H2,12,13,16,17)/t4-,5+,6+/m0/s1" 3ZO InChIKey InChI 1.03 RTWWRSBEQVIVBY-KVQBGUIXSA-N 3ZO SMILES_CANONICAL CACTVS 3.385 "O[C@H]1C[C@@H](O[C@@H]1CO[P](O)(O)=O)n2cnc3C(=O)NC(=O)Nc23" 3ZO SMILES CACTVS 3.385 "O[CH]1C[CH](O[CH]1CO[P](O)(O)=O)n2cnc3C(=O)NC(=O)Nc23" 3ZO SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "c1nc2c(n1[C@H]3C[C@@H]([C@H](O3)COP(=O)(O)O)O)NC(=O)NC2=O" 3ZO SMILES "OpenEye OEToolkits" 1.7.6 "c1nc2c(n1C3CC(C(O3)COP(=O)(O)O)O)NC(=O)NC2=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 3ZO "SYSTEMATIC NAME" ACDLabs 12.01 "2'-deoxy-5'-2,3-dihydroxanthylic acid" 3ZO "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "[(2R,3S,5R)-5-[2,6-bis(oxidanylidene)-3H-purin-9-yl]-3-oxidanyl-oxolan-2-yl]methyl 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 3ZO "Create component" 2014-12-24 RCSB 3ZO "Modify name" 2015-04-15 RCSB 3ZO "Modify synonyms" 2015-04-15 RCSB 3ZO "Initial release" 2015-10-14 RCSB 3ZO "Modify synonyms" 2020-06-05 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id 3ZO _pdbx_chem_comp_synonyms.name "2'-deoxy-5'-2,3-dihydroxanthylic acid" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##