data_NCU # _chem_comp.id NCU _chem_comp.name "[(1R,5R,7R,8S)-7-(4-amino-5-methyl-2-oxopyrimidin-1(2H)-yl)-8-hydroxy-3-methyl-2,6-dioxa-3-azabicyclo[3.2.1]oct-5-yl]methyl dihydrogen phosphate" _chem_comp.type "DNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C12 H19 N4 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 2014-08-05 _chem_comp.pdbx_modified_date 2015-08-14 _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 378.275 _chem_comp.one_letter_code ? _chem_comp.three_letter_code NCU _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 4U6K _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 NCU N1 N1 N 0 1 N N N 43.570 16.153 39.578 2.327 0.002 0.368 N1 NCU 1 NCU C7 C1 C 0 1 N N N 40.597 18.314 39.124 2.715 -3.528 -0.786 C7 NCU 2 NCU C6 C2 C 0 1 N N N 42.754 17.213 39.288 2.026 -1.238 -0.111 C6 NCU 3 NCU C5 C3 C 0 1 N N N 41.433 17.148 39.514 3.017 -2.148 -0.260 C5 NCU 4 NCU C4 C4 C 0 1 N N N 40.923 15.943 40.075 4.335 -1.786 0.086 C4 NCU 5 NCU C2 C5 C 0 1 N N N 43.047 15.000 40.154 3.595 0.317 0.689 C2 NCU 6 NCU O2 O1 O 0 1 N N N 43.820 14.068 40.429 3.846 1.432 1.117 O2 NCU 7 NCU P P1 P 0 1 N N N 44.224 21.262 37.383 -4.083 -1.473 0.250 P NCU 8 NCU OP1 O2 O 0 1 N N N 42.628 21.281 37.377 -4.930 -1.151 -0.920 OP1 NCU 9 NCU OP2 O3 O 0 1 N N N 45.047 21.744 36.095 -3.527 -2.978 0.112 OP2 NCU 10 NCU "O5'" O4 O 0 1 N N N 44.603 19.669 37.457 -2.843 -0.447 0.314 "O5'" NCU 11 NCU N3 N2 N 0 1 N N N 41.720 14.921 40.393 4.580 -0.567 0.548 N3 NCU 12 NCU N4 N3 N 0 1 N N N 39.613 15.800 40.289 5.361 -2.692 -0.055 N4 NCU 13 NCU "C2'" C6 C 0 1 N N R 45.277 15.573 37.883 1.183 1.890 -0.735 "C2'" NCU 14 NCU "C5'" C7 C 0 1 N N N 45.957 19.244 37.535 -1.941 -0.248 -0.776 "C5'" NCU 15 NCU "C4'" C8 C 0 1 N N R 46.023 17.782 37.911 -0.887 0.788 -0.382 "C4'" NCU 16 NCU "O4'" O5 O 0 1 N N N 45.442 17.544 39.213 -0.002 0.344 0.665 "O4'" NCU 17 NCU "C1'" C9 C 0 1 N N R 45.006 16.178 39.262 1.265 0.999 0.528 "C1'" NCU 18 NCU "C3'" C10 C 0 1 N N S 45.271 16.812 37.015 0.063 1.176 -1.548 "C3'" NCU 19 NCU "O3'" O6 O 0 1 N N N 45.703 16.654 35.670 -0.571 2.074 -2.462 "O3'" NCU 20 NCU "O2'" O7 O 0 1 N N N 46.634 15.040 37.877 0.641 3.156 -0.309 "O2'" NCU 21 NCU "C6'" C11 C 0 1 N N N 47.523 17.322 38.043 -1.526 2.141 0.124 "C6'" NCU 22 NCU "N6'" N4 N 0 1 N N N 47.667 15.863 38.404 -0.461 3.010 0.645 "N6'" NCU 23 NCU "C7'" C12 C 0 1 N N N 48.921 15.278 37.958 -0.996 4.322 1.036 "C7'" NCU 24 NCU H1 H1 H 0 1 N N N 39.545 18.110 39.371 2.803 -3.529 -1.873 H1 NCU 25 NCU H2 H2 H 0 1 N N N 40.936 19.207 39.670 3.424 -4.241 -0.364 H2 NCU 26 NCU H3 H3 H 0 1 N N N 40.692 18.488 38.042 1.702 -3.811 -0.503 H3 NCU 27 NCU HOP2 H4 H 0 0 N N N 43.179 18.114 38.872 1.008 -1.491 -0.368 HOP2 NCU 28 NCU H4 H6 H 0 1 N N N 44.441 22.010 35.413 -2.963 -3.258 0.845 H4 NCU 29 NCU H41 H7 H 0 1 N N N 39.260 14.948 40.675 5.178 -3.583 -0.393 H41 NCU 30 NCU H42 H8 H 0 1 N N N 38.985 16.545 40.063 6.267 -2.440 0.183 H42 NCU 31 NCU "H2'" H9 H 0 1 N N N 44.512 14.840 37.586 2.128 1.979 -1.272 "H2'" NCU 32 NCU "H5'" H10 H 0 1 N N N 46.441 19.390 36.558 -1.451 -1.190 -1.020 "H5'" NCU 33 NCU "H5''" H11 H 0 0 N N N 46.482 19.839 38.297 -2.494 0.109 -1.645 "H5''" NCU 34 NCU "H1'" H12 H 0 1 N N N 45.570 15.618 40.022 1.461 1.615 1.406 "H1'" NCU 35 NCU "H3'" H13 H 0 1 N N N 44.229 17.164 36.986 0.445 0.294 -2.062 "H3'" NCU 36 NCU "HO3'" H14 H 0 0 N Y N 45.658 17.491 35.222 0.025 2.443 -3.128 "HO3'" NCU 37 NCU H15 H15 H 0 1 N N N 48.028 17.496 37.081 -2.029 2.640 -0.704 H15 NCU 38 NCU H16 H16 H 0 1 N N N 48.006 17.925 38.826 -2.244 1.932 0.917 H16 NCU 39 NCU H17 H17 H 0 1 N N N 48.714 14.383 37.352 -1.429 4.812 0.164 H17 NCU 40 NCU H18 H18 H 0 1 N N N 49.473 16.012 37.352 -1.765 4.188 1.796 H18 NCU 41 NCU H19 H19 H 0 1 N N N 49.526 14.996 38.833 -0.191 4.938 1.437 H19 NCU 42 NCU OP3 OP3 O 0 1 N Y N 44.841 21.897 38.724 -4.956 -1.345 1.597 OP3 NCU 43 NCU HOP3 HOP3 H 0 0 N N N 44.136 22.180 39.294 -5.721 -1.935 1.627 HOP3 NCU 44 # 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 NCU "O3'" "C3'" SING N N 1 NCU OP2 P SING N N 2 NCU "C3'" "C2'" SING N N 3 NCU "C3'" "C4'" SING N N 4 NCU OP1 P DOUB N N 5 NCU P "O5'" SING N N 6 NCU "O5'" "C5'" SING N N 7 NCU "C5'" "C4'" SING N N 8 NCU "O2'" "C2'" SING N N 9 NCU "O2'" "N6'" SING N N 10 NCU "C2'" "C1'" SING N N 11 NCU "C4'" "C6'" SING N N 12 NCU "C4'" "O4'" SING N N 13 NCU "C7'" "N6'" SING N N 14 NCU "C6'" "N6'" SING N N 15 NCU C7 C5 SING N N 16 NCU "O4'" "C1'" SING N N 17 NCU "C1'" N1 SING N N 18 NCU C6 C5 DOUB N N 19 NCU C6 N1 SING N N 20 NCU C5 C4 SING N N 21 NCU N1 C2 SING N N 22 NCU C4 N4 SING N N 23 NCU C4 N3 DOUB N N 24 NCU C2 N3 SING N N 25 NCU C2 O2 DOUB N N 26 NCU C7 H1 SING N N 27 NCU C7 H2 SING N N 28 NCU C7 H3 SING N N 29 NCU C6 HOP2 SING N N 30 NCU OP2 H4 SING N N 31 NCU N4 H41 SING N N 32 NCU N4 H42 SING N N 33 NCU "C2'" "H2'" SING N N 34 NCU "C5'" "H5'" SING N N 35 NCU "C5'" "H5''" SING N N 36 NCU "C1'" "H1'" SING N N 37 NCU "C3'" "H3'" SING N N 38 NCU "O3'" "HO3'" SING N N 39 NCU "C6'" H15 SING N N 40 NCU "C6'" H16 SING N N 41 NCU "C7'" H17 SING N N 42 NCU "C7'" H18 SING N N 43 NCU "C7'" H19 SING N N 44 NCU P OP3 SING N N 45 NCU 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 NCU SMILES ACDLabs 12.01 "O=C1N=C(N)C(=CN1C3OC2(C(O)C3ON(C)C2)COP(=O)(O)O)C" NCU InChI InChI 1.03 "InChI=1S/C12H19N4O8P/c1-6-3-16(11(18)14-9(6)13)10-7-8(17)12(23-10,4-15(2)24-7)5-22-25(19,20)21/h3,7-8,10,17H,4-5H2,1-2H3,(H2,13,14,18)(H2,19,20,21)/t7-,8+,10-,12-/m1/s1" NCU InChIKey InChI 1.03 NFVTVBMMWKQGEV-UJYYTQATSA-N NCU SMILES_CANONICAL CACTVS 3.385 "CN1C[C@]2(CO[P](O)(O)=O)O[C@H]([C@H](O1)[C@@H]2O)N3C=C(C)C(=NC3=O)N" NCU SMILES CACTVS 3.385 "CN1C[C]2(CO[P](O)(O)=O)O[CH]([CH](O1)[CH]2O)N3C=C(C)C(=NC3=O)N" NCU SMILES_CANONICAL "OpenEye OEToolkits" 1.9.2 "CC1=CN(C(=O)N=C1N)[C@H]2[C@H]3[C@@H]([C@@](O2)(CN(O3)C)COP(=O)(O)O)O" NCU SMILES "OpenEye OEToolkits" 1.9.2 "CC1=CN(C(=O)N=C1N)C2C3C(C(O2)(CN(O3)C)COP(=O)(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 NCU "SYSTEMATIC NAME" ACDLabs 12.01 "[(1R,5R,7R,8S)-7-(4-amino-5-methyl-2-oxopyrimidin-1(2H)-yl)-8-hydroxy-3-methyl-2,6-dioxa-3-azabicyclo[3.2.1]oct-5-yl]methyl dihydrogen phosphate" NCU "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.9.2 "[(1R,5R,7R,8S)-7-(4-azanyl-5-methyl-2-oxidanylidene-pyrimidin-1-yl)-3-methyl-8-oxidanyl-2,6-dioxa-3-azabicyclo[3.2.1]octan-5-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 NCU "Create component" 2014-08-05 PDBJ NCU "Modify descriptor" 2014-09-05 RCSB NCU "Initial release" 2015-08-19 RCSB #