data_YCO # _chem_comp.id YCO _chem_comp.name "3-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-1H-pyrimido[5,4-b][1,4]benzoxazin-2(3H)-one" _chem_comp.type "DNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C15 H16 N3 O8 P" _chem_comp.mon_nstd_parent_comp_id DC _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2011-02-10 _chem_comp.pdbx_modified_date 2012-02-03 _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 397.277 _chem_comp.one_letter_code ? _chem_comp.three_letter_code YCO _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 3QNN _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 YCO P P P 0 1 N N N -7.545 0.889 31.626 5.509 1.560 0.130 P YCO 1 YCO N1 N1 N 0 1 N N N -4.365 2.951 26.512 -0.733 -0.877 0.295 N1 YCO 2 YCO C2 C2 C 0 1 N N N -3.557 3.250 25.393 -0.742 -0.473 -0.985 C2 YCO 3 YCO O2 O2 O 0 1 N N N -3.574 2.405 24.342 0.276 -0.571 -1.644 O2 YCO 4 YCO N3 N3 N 0 1 N N N -2.895 4.426 25.272 -1.848 0.038 -1.561 N3 YCO 5 YCO C4 C4 C 0 1 N N N -2.876 5.320 26.278 -3.009 0.154 -0.820 C4 YCO 6 YCO C5 C5 C 0 1 N N N -3.613 5.018 27.534 -2.998 -0.288 0.579 C5 YCO 7 YCO C6 C6 C 0 1 N N N -4.291 3.809 27.639 -1.861 -0.794 1.091 C6 YCO 8 YCO N7 N7 N 0 1 N N N -2.190 6.475 26.173 -4.109 0.645 -1.341 N7 YCO 9 YCO C8 C8 C 0 1 Y N N -2.185 7.375 27.193 -5.244 0.748 -0.585 C8 YCO 10 YCO C9 C9 C 0 1 Y N N -1.475 8.571 27.046 -6.407 1.273 -1.152 C9 YCO 11 YCO "C1'" "C1'" C 0 1 N N R -4.878 1.554 26.657 0.502 -1.424 0.862 "C1'" YCO 12 YCO C10 C10 C 0 1 Y N N -1.448 9.504 28.086 -7.556 1.378 -0.394 C10 YCO 13 YCO C11 C11 C 0 1 Y N N -2.141 9.249 29.274 -7.561 0.966 0.926 C11 YCO 14 YCO C12 C12 C 0 1 Y N N -2.853 8.056 29.424 -6.414 0.444 1.499 C12 YCO 15 YCO C13 C13 C 0 1 Y N N -2.878 7.114 28.388 -5.254 0.332 0.752 C13 YCO 16 YCO O14 O14 O 0 1 N N N -3.583 5.938 28.553 -4.130 -0.182 1.323 O14 YCO 17 YCO "C2'" "C2'" C 0 1 N N N -3.789 0.514 26.827 0.870 -2.738 0.146 "C2'" YCO 18 YCO "C3'" "C3'" C 0 1 N N S -3.823 0.265 28.314 2.280 -2.473 -0.434 "C3'" YCO 19 YCO "O3'" "O3'" O 0 1 N N N -3.412 -1.059 28.643 3.121 -3.618 -0.275 "O3'" YCO 20 YCO "C4'" "C4'" C 0 1 N N R -5.268 0.482 28.692 2.776 -1.296 0.445 "C4'" YCO 21 YCO "O4'" "O4'" O 0 1 N N N -5.753 1.487 27.800 1.587 -0.505 0.651 "O4'" YCO 22 YCO "C5'" "C5'" C 0 1 N N N -5.309 0.971 30.125 3.843 -0.485 -0.294 "C5'" YCO 23 YCO "O5'" "O5'" O 0 1 N N N -6.581 1.527 30.368 4.365 0.520 0.578 "O5'" YCO 24 YCO OP1 OP1 O 0 1 N N N -9.311 1.241 31.615 5.076 2.274 -1.092 OP1 YCO 25 YCO OP2 OP2 O 0 1 N N N -6.887 -0.486 32.655 5.760 2.624 1.313 OP2 YCO 26 YCO OP3 OP3 O 0 1 N Y N -7.160 2.060 32.825 6.874 0.761 -0.170 O8 YCO 27 YCO HN3 HN3 H 0 1 N N N -2.412 4.633 24.421 -1.829 0.323 -2.488 HN3 YCO 28 YCO H6 H6 H 0 1 N N N -4.757 3.525 28.571 -1.828 -1.130 2.117 H6 YCO 29 YCO H9 H9 H 0 1 N N N -0.946 8.774 26.126 -6.407 1.596 -2.182 H9 YCO 30 YCO "H1'" "H1'" H 0 1 N N N -5.405 1.320 25.720 0.371 -1.607 1.928 "H1'" YCO 31 YCO H10 H10 H 0 1 N N N -0.892 10.423 27.972 -8.455 1.785 -0.834 H10 YCO 32 YCO H11 H11 H 0 1 N N N -2.126 9.974 30.075 -8.464 1.051 1.513 H11 YCO 33 YCO H12 H12 H 0 1 N N N -3.386 7.860 30.342 -6.424 0.124 2.531 H12 YCO 34 YCO "H2'" "H2'" H 0 1 N N N -3.997 -0.400 26.251 0.899 -3.565 0.856 "H2'" YCO 35 YCO "H2'A" "H2'A" H 0 0 N N N -2.809 0.884 26.493 0.161 -2.947 -0.655 "H2'A" YCO 36 YCO "H3'" "H3'" H 0 1 N N N -3.132 0.929 28.854 2.221 -2.179 -1.482 "H3'" YCO 37 YCO "HO3'" "HO3'" H 0 0 N Y N -3.447 -1.177 29.585 2.802 -4.407 -0.734 "HO3'" YCO 38 YCO "H4'" "H4'" H 0 1 N N N -5.879 -0.430 28.618 3.165 -1.664 1.395 "H4'" YCO 39 YCO "H5'" "H5'" H 0 1 N N N -5.132 0.130 30.812 4.649 -1.146 -0.610 "H5'" YCO 40 YCO "H5'A" "H5'A" H 0 0 N N N -4.532 1.734 30.282 3.397 -0.011 -1.168 "H5'A" YCO 41 YCO HOP2 HOP2 H 0 0 N N N -6.987 -1.307 32.188 6.438 3.283 1.112 HOP2 YCO 42 YCO HOP3 HOP3 H 0 0 N Y N -7.953 2.507 33.097 7.217 0.269 0.589 H17 YCO 43 # 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 YCO P OP2 SING N N 1 YCO P OP3 SING N N 2 YCO N1 "C1'" SING N N 3 YCO N1 C6 SING N N 4 YCO C2 N1 SING N N 5 YCO O2 C2 DOUB N N 6 YCO N3 C2 SING N N 7 YCO N3 C4 SING N N 8 YCO N3 HN3 SING N N 9 YCO C4 C5 SING N N 10 YCO C5 C6 DOUB N N 11 YCO C5 O14 SING N N 12 YCO C6 H6 SING N N 13 YCO N7 C4 DOUB N N 14 YCO N7 C8 SING N N 15 YCO C8 C13 SING Y N 16 YCO C9 C8 DOUB Y N 17 YCO C9 C10 SING Y N 18 YCO C9 H9 SING N N 19 YCO "C1'" "C2'" SING N N 20 YCO "C1'" "O4'" SING N N 21 YCO "C1'" "H1'" SING N N 22 YCO C10 C11 DOUB Y N 23 YCO C10 H10 SING N N 24 YCO C11 C12 SING Y N 25 YCO C11 H11 SING N N 26 YCO C12 H12 SING N N 27 YCO C13 C12 DOUB Y N 28 YCO C13 O14 SING N N 29 YCO "C2'" "C3'" SING N N 30 YCO "C2'" "H2'" SING N N 31 YCO "C2'" "H2'A" SING N N 32 YCO "C3'" "O3'" SING N N 33 YCO "C3'" "C4'" SING N N 34 YCO "C3'" "H3'" SING N N 35 YCO "O3'" "HO3'" SING N N 36 YCO "C4'" "C5'" SING N N 37 YCO "C4'" "H4'" SING N N 38 YCO "O4'" "C4'" SING N N 39 YCO "C5'" "O5'" SING N N 40 YCO "C5'" "H5'" SING N N 41 YCO "C5'" "H5'A" SING N N 42 YCO "O5'" P SING N N 43 YCO OP1 P DOUB N N 44 YCO OP2 HOP2 SING N N 45 YCO OP3 HOP3 SING N N 46 # 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 YCO SMILES ACDLabs 12.01 "O=P(O)(O)OCC4OC(N2C(=O)NC1=Nc3ccccc3OC1=C2)CC4O" YCO SMILES_CANONICAL CACTVS 3.370 "O[C@H]1C[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C=C3Oc4ccccc4N=C3NC2=O" YCO SMILES CACTVS 3.370 "O[CH]1C[CH](O[CH]1CO[P](O)(O)=O)N2C=C3Oc4ccccc4N=C3NC2=O" YCO SMILES_CANONICAL "OpenEye OEToolkits" 1.7.0 "c1ccc2c(c1)N=C3C(=CN(C(=O)N3)[C@H]4C[C@@H]([C@H](O4)COP(=O)(O)O)O)O2" YCO SMILES "OpenEye OEToolkits" 1.7.0 "c1ccc2c(c1)N=C3C(=CN(C(=O)N3)C4CC(C(O4)COP(=O)(O)O)O)O2" YCO InChI InChI 1.03 "InChI=1S/C15H16N3O8P/c19-9-5-13(26-12(9)7-24-27(21,22)23)18-6-11-14(17-15(18)20)16-8-3-1-2-4-10(8)25-11/h1-4,6,9,12-13,19H,5,7H2,(H,16,17,20)(H2,21,22,23)/t9-,12+,13+/m0/s1" YCO InChIKey InChI 1.03 CEYLCTLUVICBGV-ZWKOPEQDSA-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 YCO "SYSTEMATIC NAME" ACDLabs 12.01 "3-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-1H-pyrimido[5,4-b][1,4]benzoxazin-2(3H)-one" YCO "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.0 "[(2R,3S,5R)-3-hydroxy-5-(2-oxo-1H-pyrimido[5,4-b][1,4]benzoxazin-3-yl)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 YCO "Other modification" 2011-02-10 RCSB YCO "Modify descriptor" 2011-06-04 RCSB #