data_0KZ # _chem_comp.id 0KZ _chem_comp.name ;[(1R,2S,4S,5S)-2-hydroxy-4-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)bicyclo[3.1.0]hex-1-yl]methyl dihydrogen phosphate ; _chem_comp.type "DNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C12 H17 N2 O7 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "2'-exo-methanocarba-thymidine monophosphate; North-methanocarba-thymidine monophosphate" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2012-02-07 _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 332.246 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 0KZ _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag Y _chem_comp.pdbx_ideal_coordinates_details Corina _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 4DKZ _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 0KZ C2 C2 C 0 1 N N N -3.278 15.405 5.776 -2.486 -0.949 0.275 C2 NC1 1 0KZ N3 N3 N 0 1 N N N -3.434 15.224 7.174 -3.575 -1.740 0.290 N3 NC1 2 0KZ C4 C4 C 0 1 N N N -4.266 14.290 7.829 -4.796 -1.220 0.055 C4 NC1 3 0KZ C5 C5 C 0 1 N N N -5.051 13.411 6.960 -4.922 0.165 -0.208 C5 NC1 4 0KZ C6 C6 C 0 1 N N N -4.916 13.572 5.635 -3.813 0.936 -0.218 C6 NC1 5 0KZ C7 C7 C 0 1 N N N -5.970 12.372 7.517 -6.275 0.772 -0.475 C7 NC1 6 0KZ P P P 0 1 N N N -8.083 10.810 3.687 4.623 -0.694 0.007 P NC1 7 0KZ OP1 OP1 O 0 1 N N N -8.301 9.909 2.533 4.311 -2.050 0.512 OP1 NC1 8 0KZ OP2 OP2 O 0 1 N N N -7.907 10.309 5.067 5.202 -0.799 -1.492 OP2 NC1 9 0KZ "O5'" "O5'" O 0 1 N N N -6.884 11.846 3.440 3.283 0.199 0.004 "O5'" NC1 10 0KZ "C5'" "C5'" C 0 1 N N N -6.578 12.348 2.119 2.085 -0.198 -0.665 "C5'" NC1 11 0KZ "C4'" "C4'" C 0 1 N N R -5.406 13.382 1.858 1.012 0.874 -0.469 "C4'" NC1 12 0KZ "C6'" "C6'" C 0 1 N N S -5.488 14.526 2.904 -0.399 0.713 -1.062 "C6'" NC1 13 0KZ "C7'" "C7'" C 0 1 N N N -5.333 14.811 1.374 0.598 1.746 -1.656 "C7'" NC1 14 0KZ "C1'" "C1'" C 0 1 N N S -4.006 14.616 3.441 -1.388 1.204 0.015 "C1'" NC1 15 0KZ N1 N1 N 0 1 N N N -4.076 14.520 4.981 -2.592 0.368 0.026 N1 NC1 16 0KZ O2 O2 O 0 1 N N N -2.525 16.250 5.325 -1.391 -1.432 0.493 O2 NC1 17 0KZ O4 O4 O 0 1 N N N -4.290 14.260 9.055 -5.782 -1.935 0.069 O4 NC1 18 0KZ "C2'" "C2'" C 0 1 N N N -3.246 13.295 3.054 -0.610 1.050 1.345 "C2'" NC1 19 0KZ "C3'" "C3'" C 0 1 N N S -4.269 12.396 2.332 0.830 1.445 0.953 "C3'" NC1 20 0KZ "O3'" "O3'" O 0 1 N N N -3.819 11.755 1.120 0.951 2.869 0.940 "O3'" NC1 21 0KZ H1 H1 H 0 1 N N N -2.894 15.826 7.762 -3.480 -2.689 0.471 H1 NC1 22 0KZ H2 H2 H 0 1 N N N -5.500 12.920 5.003 -3.889 1.994 -0.417 H2 NC1 23 0KZ H3 H3 H 0 1 N N N -5.936 12.403 8.616 -7.038 -0.005 -0.424 H3 NC1 24 0KZ H4 H4 H 0 1 N N N -6.997 12.570 7.176 -6.485 1.536 0.274 H4 NC1 25 0KZ H5 H5 H 0 1 N N N -5.654 11.378 7.168 -6.282 1.224 -1.467 H5 NC1 26 0KZ H7 H7 H 0 1 N N N -7.958 9.360 5.069 5.428 0.054 -1.887 H7 NC1 27 0KZ H8 H8 H 0 1 N N N -7.498 12.828 1.753 2.286 -0.320 -1.730 H8 NC1 28 0KZ H9 H9 H 0 1 N N N -6.353 11.467 1.501 1.734 -1.143 -0.251 H9 NC1 29 0KZ H10 H10 H 0 1 N N N -6.379 14.773 3.499 -0.677 -0.175 -1.630 H10 NC1 30 0KZ H11 H11 H 0 1 N N N -4.385 15.210 0.984 0.401 2.800 -1.461 H11 NC1 31 0KZ H12 H12 H 0 1 N N N -6.172 15.242 0.809 1.048 1.524 -2.624 H12 NC1 32 0KZ H13 H13 H 0 1 N N N -3.486 15.520 3.090 -1.652 2.248 -0.157 H13 NC1 33 0KZ H14 H14 H 0 1 N N N -2.871 12.793 3.958 -1.006 1.724 2.105 H14 NC1 34 0KZ H15 H15 H 0 1 N N N -2.403 13.524 2.386 -0.640 0.018 1.693 H15 NC1 35 0KZ H16 H16 H 0 1 N N N -4.690 11.665 3.038 1.556 1.005 1.636 H16 NC1 36 0KZ H17 H17 H 0 1 N N N -3.126 11.139 1.326 0.845 3.280 1.808 H17 NC1 37 0KZ OP3 OP3 O 0 1 N Y N ? ? ? 5.724 -0.007 0.960 OP3 NC1 38 0KZ H19 H19 H 0 1 N Y N ? ? ? 6.559 -0.492 1.010 H19 NC1 39 # # 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 0KZ "O3'" "C3'" SING N N 1 0KZ "C7'" "C4'" SING N N 2 0KZ "C7'" "C6'" SING N N 3 0KZ "C4'" "C5'" SING N N 4 0KZ "C4'" "C3'" SING N N 5 0KZ "C4'" "C6'" SING N N 6 0KZ "C5'" "O5'" SING N N 7 0KZ "C3'" "C2'" SING N N 8 0KZ OP1 P DOUB N N 9 0KZ "C6'" "C1'" SING N N 10 0KZ "C2'" "C1'" SING N N 11 0KZ "O5'" P SING N N 12 0KZ "C1'" N1 SING N N 13 0KZ P OP2 SING N N 14 0KZ N1 C6 SING N N 15 0KZ N1 C2 SING N N 16 0KZ O2 C2 DOUB N N 17 0KZ C6 C5 DOUB N N 18 0KZ C2 N3 SING N N 19 0KZ C5 C7 SING N N 20 0KZ C5 C4 SING N N 21 0KZ N3 C4 SING N N 22 0KZ C4 O4 DOUB N N 23 0KZ N3 H1 SING N N 24 0KZ C6 H2 SING N N 25 0KZ C7 H3 SING N N 26 0KZ C7 H4 SING N N 27 0KZ C7 H5 SING N N 28 0KZ OP2 H7 SING N N 29 0KZ "C5'" H8 SING N N 30 0KZ "C5'" H9 SING N N 31 0KZ "C6'" H10 SING N N 32 0KZ "C7'" H11 SING N N 33 0KZ "C7'" H12 SING N N 34 0KZ "C1'" H13 SING N N 35 0KZ "C2'" H14 SING N N 36 0KZ "C2'" H15 SING N N 37 0KZ "C3'" H16 SING N N 38 0KZ "O3'" H17 SING N N 39 0KZ P OP3 SING N N 40 0KZ OP3 H19 SING N N 41 # # 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 0KZ SMILES ACDLabs 12.01 "O=P(O)(O)OCC32C(C(N1C=C(C(=O)NC1=O)C)CC2O)C3" 0KZ InChI InChI 1.03 "InChI=1S/C12H17N2O7P/c1-6-4-14(11(17)13-10(6)16)8-2-9(15)12(3-7(8)12)5-21-22(18,19)20/h4,7-9,15H,2-3,5H2,1H3,(H,13,16,17)(H2,18,19,20)/t7-,8+,9+,12+/m1/s1" 0KZ InChIKey InChI 1.03 UGXPFKYDADDXLN-ARHDFHRDSA-N 0KZ SMILES_CANONICAL CACTVS 3.370 "CC1=CN([C@H]2C[C@H](O)[C@]3(CO[P](O)(O)=O)C[C@H]23)C(=O)NC1=O" 0KZ SMILES CACTVS 3.370 "CC1=CN([CH]2C[CH](O)[C]3(CO[P](O)(O)=O)C[CH]23)C(=O)NC1=O" 0KZ SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H](C3([C@@H]2C3)COP(=O)(O)O)O" 0KZ SMILES "OpenEye OEToolkits" 1.7.6 "CC1=CN(C(=O)NC1=O)C2CC(C3(C2C3)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 0KZ "SYSTEMATIC NAME" ACDLabs 12.01 "[(1R,2S,4S,5S)-2-hydroxy-4-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)bicyclo[3.1.0]hex-1-yl]methyl dihydrogen phosphate" 0KZ "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "[(1S,2S,4S)-2-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-4-oxidanyl-5-bicyclo[3.1.0]hexanyl]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 0KZ "Create component" 2012-02-07 RCSB 0KZ "Modify synonyms" 2020-06-05 PDBE # # loop_ _pdbx_chem_comp_synonyms.ordinal _pdbx_chem_comp_synonyms.comp_id _pdbx_chem_comp_synonyms.name _pdbx_chem_comp_synonyms.provenance _pdbx_chem_comp_synonyms.type 1 0KZ "2'-exo-methanocarba-thymidine monophosphate" ? ? 2 0KZ "North-methanocarba-thymidine monophosphate" ? ? ##