data_D00 # _chem_comp.id D00 _chem_comp.name ;2'-deoxy-N-ethylcytidine 5'-(dihydrogen phosphate) ; _chem_comp.type "DNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C11 H18 N3 O7 P" _chem_comp.mon_nstd_parent_comp_id DC _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2014-06-06 _chem_comp.pdbx_modified_date 2014-06-20 _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 335.250 _chem_comp.one_letter_code ? _chem_comp.three_letter_code D00 _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 1N4B _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 D00 P P P 0 1 N N N 0.549 -8.842 16.532 4.341 1.409 0.091 P D00 1 D00 OP1 OP1 O 0 1 N N N -0.455 -9.916 16.358 5.631 0.707 -0.567 OP1 D00 2 D00 OP2 OP2 O 0 1 N N N 1.771 -8.830 15.697 3.762 2.376 -0.869 OP2 D00 3 D00 "O5'" "O5'" O 0 1 N N N -0.194 -7.430 16.344 3.243 0.287 0.450 "O5'" D00 4 D00 "C5'" "C5'" C 0 1 N N N -1.378 -7.220 17.103 2.581 -0.499 -0.542 "C5'" D00 5 D00 "C4'" "C4'" C 0 1 N N R -1.745 -5.752 17.178 1.607 -1.463 0.138 "C4'" D00 6 D00 "O4'" "O4'" O 0 1 N N N -0.638 -4.983 17.635 0.530 -0.737 0.769 "O4'" D00 7 D00 "C3'" "C3'" C 0 1 N N S -2.228 -5.031 15.951 0.882 -2.340 -0.915 "C3'" D00 8 D00 "O3'" "O3'" O 0 1 N N N -3.510 -4.437 16.080 1.655 -3.500 -1.230 "O3'" D00 9 D00 "C2'" "C2'" C 0 1 N N N -1.129 -4.019 15.769 -0.420 -2.728 -0.173 "C2'" D00 10 D00 "C1'" "C1'" C 0 1 N N R -0.785 -3.634 17.183 -0.562 -1.657 0.926 "C1'" D00 11 D00 N1 N1 N 0 1 N N N 0.591 -3.131 17.356 -1.836 -0.950 0.770 N1 D00 12 D00 C2 C2 C 0 1 N N N 0.851 -2.004 18.107 -2.054 -0.197 -0.324 C2 D00 13 D00 O2 O2 O 0 1 N N N -0.054 -1.350 18.620 -1.185 -0.112 -1.176 O2 D00 14 D00 N3 N3 N 0 1 N N N 2.154 -1.635 18.254 -3.202 0.456 -0.492 N3 D00 15 D00 C4 C4 C 0 1 N N N 3.199 -2.298 17.713 -4.163 0.381 0.420 C4 D00 16 D00 N4 N4 N 0 1 N N N 4.479 -2.164 18.213 -5.346 1.059 0.236 N4 D00 17 D00 C5 C5 C 0 1 N N N 2.888 -3.464 16.929 -3.967 -0.400 1.577 C5 D00 18 D00 C6 C6 C 0 1 N N N 1.600 -3.830 16.786 -2.796 -1.062 1.730 C6 D00 19 D00 C10 C10 C 0 1 N N N 5.345 -0.046 19.346 -6.934 2.512 -0.927 C10 D00 20 D00 C11 C11 C 0 1 N N N 5.193 -0.881 18.290 -5.546 1.868 -0.969 C11 D00 21 D00 OP3 OP3 O 0 1 N Y N 1.004 -8.818 18.080 4.777 2.183 1.434 OP3 D00 22 D00 H1 H1 H 0 1 N N N -0.167 -10.512 15.677 6.062 0.059 0.008 H1 D00 23 D00 "H5''" "H5''" H 0 0 N N N -2.206 -7.770 16.631 2.032 0.156 -1.218 "H5''" D00 24 D00 "H5'" "H5'" H 0 1 N N N -1.219 -7.600 18.123 3.320 -1.068 -1.107 "H5'" D00 25 D00 "H4'" "H4'" H 0 1 N N N -2.544 -5.667 17.930 2.128 -2.085 0.866 "H4'" D00 26 D00 "H3'" "H3'" H 0 1 N N N -2.217 -5.727 15.099 0.662 -1.765 -1.814 "H3'" D00 27 D00 "HO3'" "HO3'" H 0 0 N Y N -4.164 -5.116 16.192 1.243 -4.081 -1.885 "HO3'" D00 28 D00 "H2''" "H2''" H 0 0 N N N -0.262 -4.464 15.259 -1.271 -2.693 -0.853 "H2''" D00 29 D00 "H2'" "H2'" H 0 1 N N N -1.484 -3.149 15.198 -0.325 -3.720 0.271 "H2'" D00 30 D00 "H1'" "H1'" H 0 1 N N N -1.560 -3.043 17.692 -0.517 -2.126 1.909 "H1'" D00 31 D00 H41 H41 H 0 1 N N N 4.946 -2.985 18.541 -6.047 1.002 0.904 H41 D00 32 D00 H5 H5 H 0 1 N N N 3.676 -4.037 16.462 -4.739 -0.471 2.329 H5 D00 33 D00 H6 H6 H 0 1 N N N 1.366 -4.706 16.200 -2.621 -1.667 2.608 H6 D00 34 D00 H12 H12 H 0 1 N N N 5.942 0.827 19.041 -7.695 1.732 -0.881 H12 D00 35 D00 H11 H11 H 0 1 N N N 4.357 0.289 19.694 -7.012 3.148 -0.045 H11 D00 36 D00 H8 H8 H 0 1 N N N 5.860 -0.576 20.161 -7.083 3.114 -1.823 H8 D00 37 D00 H13 H13 H 0 1 N N N 6.222 -1.123 17.985 -4.786 2.648 -1.014 H13 D00 38 D00 H14 H14 H 0 1 N N N 4.718 -0.259 17.517 -5.468 1.232 -1.851 H14 D00 39 D00 H9 H9 H 0 1 N N N 1.952 -8.801 18.132 5.438 2.875 1.293 H9 D00 40 # 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 D00 OP2 P DOUB N N 1 D00 "C2'" "C3'" SING N N 2 D00 "C2'" "C1'" SING N N 3 D00 "C3'" "O3'" SING N N 4 D00 "C3'" "C4'" SING N N 5 D00 "O5'" P SING N N 6 D00 "O5'" "C5'" SING N N 7 D00 OP1 P SING N N 8 D00 C6 C5 DOUB N N 9 D00 C6 N1 SING N N 10 D00 C5 C4 SING N N 11 D00 "C5'" "C4'" SING N N 12 D00 "C4'" "O4'" SING N N 13 D00 "C1'" N1 SING N N 14 D00 "C1'" "O4'" SING N N 15 D00 N1 C2 SING N N 16 D00 C4 N4 SING N N 17 D00 C4 N3 DOUB N N 18 D00 C2 N3 SING N N 19 D00 C2 O2 DOUB N N 20 D00 N4 C11 SING N N 21 D00 C11 C10 SING N N 22 D00 P OP3 SING N N 23 D00 OP1 H1 SING N N 24 D00 "C5'" "H5''" SING N N 25 D00 "C5'" "H5'" SING N N 26 D00 "C4'" "H4'" SING N N 27 D00 "C3'" "H3'" SING N N 28 D00 "O3'" "HO3'" SING N N 29 D00 "C2'" "H2''" SING N N 30 D00 "C2'" "H2'" SING N N 31 D00 "C1'" "H1'" SING N N 32 D00 N4 H41 SING N N 33 D00 C5 H5 SING N N 34 D00 C6 H6 SING N N 35 D00 C10 H12 SING N N 36 D00 C10 H11 SING N N 37 D00 C10 H8 SING N N 38 D00 C11 H13 SING N N 39 D00 C11 H14 SING N N 40 D00 OP3 H9 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 D00 SMILES ACDLabs 12.01 "O=P(O)(O)OCC2OC(N1C(=O)N=C(NCC)C=C1)CC2O" D00 InChI InChI 1.03 "InChI=1S/C11H18N3O7P/c1-2-12-9-3-4-14(11(16)13-9)10-5-7(15)8(21-10)6-20-22(17,18)19/h3-4,7-8,10,15H,2,5-6H2,1H3,(H,12,13,16)(H2,17,18,19)/t7-,8+,10+/m0/s1" D00 InChIKey InChI 1.03 CLGIJIDGLSCEMM-QXFUBDJGSA-N D00 SMILES_CANONICAL CACTVS 3.385 "CCNC1=NC(=O)N(C=C1)[C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=O)O2" D00 SMILES CACTVS 3.385 "CCNC1=NC(=O)N(C=C1)[CH]2C[CH](O)[CH](CO[P](O)(O)=O)O2" D00 SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "CCNC1=NC(=O)N(C=C1)[C@H]2C[C@@H]([C@H](O2)COP(=O)(O)O)O" D00 SMILES "OpenEye OEToolkits" 1.7.6 "CCNC1=NC(=O)N(C=C1)C2CC(C(O2)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 D00 "SYSTEMATIC NAME" ACDLabs 12.01 ;2'-deoxy-N-ethylcytidine 5'-(dihydrogen phosphate) ; D00 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "[(2R,3S,5R)-5-[4-(ethylamino)-2-oxidanylidene-pyrimidin-1-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 D00 "Create component" 2014-06-06 PDBJ D00 "Modify linking type" 2014-06-10 PDBJ D00 "Modify parent residue" 2014-06-10 PDBJ D00 "Modify value order" 2014-06-10 PDBJ D00 "Modify name" 2014-06-10 PDBJ D00 "Modify formula" 2014-06-10 PDBJ D00 "Modify atom id" 2014-06-10 PDBJ D00 "Initial release" 2014-06-25 RCSB #