data_DDY # _chem_comp.id DDY _chem_comp.name "2',3'-DIDEOXYCYTOSINE-5'-DIPHOSPHATE" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C9 H15 N3 O9 P2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms DDCDP _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2004-04-19 _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 371.178 _chem_comp.one_letter_code ? _chem_comp.three_letter_code DDY _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 1S9F _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 DDY C4 C4 C 0 1 N N N 16.165 17.840 -5.459 5.720 -1.713 -0.249 C4 DDY 1 DDY PB PB P 0 1 N N N 20.514 15.607 1.186 -5.058 -0.877 0.440 PB DDY 2 DDY PA PA P 0 1 N N N 19.132 13.536 -0.290 -2.592 0.397 -0.601 PA DDY 3 DDY C2 C2 C 0 1 N N N 15.067 15.663 -5.521 3.994 -0.219 -0.606 C2 DDY 4 DDY C5 C5 C 0 1 N N N 16.593 17.602 -4.146 5.655 -1.453 1.135 C5 DDY 5 DDY O2 O2 O 0 1 N N N 14.418 14.816 -6.136 3.243 0.346 -1.385 O2 DDY 6 DDY O3B O3B O 0 1 N N N 21.838 14.771 0.875 -5.893 0.227 -0.084 O3B DDY 7 DDY O1B O1B O 0 1 N N N 20.075 15.239 2.546 -5.508 -1.221 1.947 O1B DDY 8 DDY O2B O2B O 0 1 N N N 20.776 17.031 0.909 -5.247 -2.180 -0.487 O2B DDY 9 DDY O3A O3A O 0 1 N N N 19.441 15.088 0.072 -3.511 -0.431 0.430 O3A DDY 10 DDY O1A O1A O 0 1 N N N 19.029 12.708 0.916 -3.324 1.599 -1.059 O1A DDY 11 DDY O2A O2A O 0 1 N N N 20.091 13.113 -1.332 -2.239 -0.531 -1.869 O2A DDY 12 DDY "O5'" "O5'" O 0 1 N N N 17.685 13.681 -0.970 -1.231 0.844 0.133 "O5'" DDY 13 DDY "C5'" "C5'" C 0 1 N N N 16.531 12.998 -0.473 -0.253 1.682 -0.486 "C5'" DDY 14 DDY "C4'" "C4'" C 0 1 N N S 15.468 12.955 -1.578 0.909 1.910 0.483 "C4'" DDY 15 DDY "O4'" "O4'" O 0 1 N N N 15.112 14.292 -2.030 1.621 0.677 0.722 "O4'" DDY 16 DDY "C3'" "C3'" C 0 1 N N N 15.996 12.392 -2.667 1.981 2.828 -0.157 "C3'" DDY 17 DDY "C2'" "C2'" C 0 1 N N N 15.758 13.102 -3.753 3.258 2.429 0.623 "C2'" DDY 18 DDY "C1'" "C1'" C 0 1 N N R 15.038 14.183 -3.479 2.933 1.033 1.190 "C1'" DDY 19 DDY N1 N1 N 0 1 N N N 15.488 15.420 -4.191 3.915 0.059 0.708 N1 DDY 20 DDY C6 C6 C 0 1 N N N 16.258 16.396 -3.513 4.744 -0.562 1.594 C6 DDY 21 DDY N4 N4 N 0 1 N N N 16.462 18.991 -6.061 6.636 -2.613 -0.742 N4 DDY 22 DDY N3 N3 N 0 1 N N N 15.407 16.875 -6.145 4.888 -1.088 -1.073 N3 DDY 23 DDY H5 H5 H 0 1 N N N 17.178 18.344 -3.624 6.322 -1.957 1.819 H5 DDY 24 DDY H1B H1B H 0 1 N N N 20.676 14.600 2.911 -6.431 -1.498 2.028 H1B DDY 25 DDY H2B H2B H 0 1 N N N 21.671 17.136 0.608 -4.728 -2.944 -0.202 H2B DDY 26 DDY H2A H2A H 0 1 N N N 20.530 12.317 -1.055 -1.758 -1.339 -1.643 H2A DDY 27 DDY "H5'1" "H5'1" H 0 0 N N N 16.804 11.973 -0.181 0.117 1.202 -1.391 "H5'1" DDY 28 DDY "H5'2" "H5'2" H 0 0 N N N 16.133 13.531 0.403 -0.705 2.641 -0.742 "H5'2" DDY 29 DDY "H4'" "H4'" H 0 1 N N N 14.603 12.417 -1.162 0.549 2.333 1.421 "H4'" DDY 30 DDY "H3'1" "H3'1" H 0 0 N N N 17.085 12.313 -2.530 2.092 2.615 -1.220 "H3'1" DDY 31 DDY "H3'2" "H3'2" H 0 0 N N N 15.555 11.393 -2.796 1.740 3.879 0.005 "H3'2" DDY 32 DDY "H2'1" "H2'1" H 0 0 N N N 16.718 13.416 -4.189 4.115 2.378 -0.049 "H2'1" DDY 33 DDY "H2'2" "H2'2" H 0 0 N N N 15.203 12.479 -4.470 3.447 3.134 1.432 "H2'2" DDY 34 DDY "H1'" "H1'" H 0 1 N N N 14.004 14.082 -3.842 2.942 1.064 2.279 "H1'" DDY 35 DDY H6 H6 H 0 1 N N N 16.589 16.211 -2.502 4.675 -0.347 2.650 H6 DDY 36 DDY HN41 HN41 H 0 0 N N N 16.146 19.163 -6.994 7.240 -3.071 -0.137 HN41 DDY 37 DDY HN42 HN42 H 0 0 N N N 17.001 19.682 -5.580 6.678 -2.789 -1.695 HN42 DDY 38 # # 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 DDY C4 C5 SING N N 1 DDY C4 N4 SING N N 2 DDY C4 N3 DOUB N N 3 DDY PB O3B DOUB N N 4 DDY PB O1B SING N N 5 DDY PB O2B SING N N 6 DDY PB O3A SING N N 7 DDY PA O3A SING N N 8 DDY PA O1A DOUB N N 9 DDY PA O2A SING N N 10 DDY PA "O5'" SING N N 11 DDY C2 O2 DOUB N N 12 DDY C2 N1 SING N N 13 DDY C2 N3 SING N N 14 DDY C5 C6 DOUB N N 15 DDY C5 H5 SING N N 16 DDY O1B H1B SING N N 17 DDY O2B H2B SING N N 18 DDY O2A H2A SING N N 19 DDY "O5'" "C5'" SING N N 20 DDY "C5'" "C4'" SING N N 21 DDY "C5'" "H5'1" SING N N 22 DDY "C5'" "H5'2" SING N N 23 DDY "C4'" "O4'" SING N N 24 DDY "C4'" "C3'" SING N N 25 DDY "C4'" "H4'" SING N N 26 DDY "O4'" "C1'" SING N N 27 DDY "C3'" "C2'" SING N N 28 DDY "C3'" "H3'1" SING N N 29 DDY "C3'" "H3'2" SING N N 30 DDY "C2'" "C1'" SING N N 31 DDY "C2'" "H2'1" SING N N 32 DDY "C2'" "H2'2" SING N N 33 DDY "C1'" N1 SING N N 34 DDY "C1'" "H1'" SING N N 35 DDY N1 C6 SING N N 36 DDY C6 H6 SING N N 37 DDY N4 HN41 SING N N 38 DDY N4 HN42 SING N N 39 # # 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 DDY SMILES ACDLabs 12.01 "O=P(O)(O)OP(=O)(O)OCC2OC(N1C(=O)N=C(N)C=C1)CC2" DDY SMILES_CANONICAL CACTVS 3.370 "NC1=NC(=O)N(C=C1)[C@H]2CC[C@@H](CO[P](O)(=O)O[P](O)(O)=O)O2" DDY SMILES CACTVS 3.370 "NC1=NC(=O)N(C=C1)[CH]2CC[CH](CO[P](O)(=O)O[P](O)(O)=O)O2" DDY SMILES_CANONICAL "OpenEye OEToolkits" 1.7.0 "C1C[C@@H](O[C@@H]1CO[P@@](=O)(O)OP(=O)(O)O)N2C=CC(=NC2=O)N" DDY SMILES "OpenEye OEToolkits" 1.7.0 "C1CC(OC1COP(=O)(O)OP(=O)(O)O)N2C=CC(=NC2=O)N" DDY InChI InChI 1.03 "InChI=1S/C9H15N3O9P2/c10-7-3-4-12(9(13)11-7)8-2-1-6(20-8)5-19-23(17,18)21-22(14,15)16/h3-4,6,8H,1-2,5H2,(H,17,18)(H2,10,11,13)(H2,14,15,16)/t6-,8+/m0/s1" DDY InChIKey InChI 1.03 FVSQWXITYSICAK-POYBYMJQSA-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 DDY "SYSTEMATIC NAME" ACDLabs 12.01 "[(2S,5R)-5-(4-amino-2-oxopyrimidin-1(2H)-yl)tetrahydrofuran-2-yl]methyl trihydrogen diphosphate" DDY "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.0 "[(2S,5R)-5-(4-azanyl-2-oxo-pyrimidin-1-yl)oxolan-2-yl]methyl phosphono hydrogen 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 DDY "Create component" 2004-04-19 RCSB DDY "Modify descriptor" 2011-06-04 RCSB DDY "Modify synonyms" 2020-06-05 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id DDY _pdbx_chem_comp_synonyms.name DDCDP _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##