data_C7R # _chem_comp.id C7R _chem_comp.name "2'-deoxy-5'-O-thiophosphonocytidine" _chem_comp.type "DNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C9 H14 N3 O6 P S" _chem_comp.mon_nstd_parent_comp_id DC _chem_comp.pdbx_synonyms "2'-deoxy-5'-O-thiophosphonocytidine (thiophospho connection isoform 1)" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2016-04-28 _chem_comp.pdbx_modified_date 2021-03-01 _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 323.263 _chem_comp.one_letter_code ? _chem_comp.three_letter_code C7R _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 5JLW _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 C7R P P1 P 0 1 N N N 2.932 15.221 -11.136 3.886 -0.560 -0.297 P C7R 1 C7R "C5'" C1 C 0 1 N N N 4.889 15.371 -12.775 1.760 0.916 0.366 "C5'" C7R 2 C7R "O5'" O1 O 0 1 N N N 3.719 14.720 -12.428 2.536 0.250 -0.632 "O5'" C7R 3 C7R "C4'" C2 C 0 1 N N R 5.363 14.960 -14.131 0.549 1.583 -0.290 "C4'" C7R 4 C7R "O4'" O2 O 0 1 N N N 6.448 15.839 -14.503 -0.380 0.588 -0.772 "O4'" C7R 5 C7R "C3'" C3 C 0 1 N N S 5.914 13.538 -14.193 -0.273 2.374 0.759 "C3'" C7R 6 C7R "O3'" O3 O 0 1 N N N 5.661 12.913 -15.460 0.243 3.696 0.920 "O3'" C7R 7 C7R "C2'" C4 C 0 1 N N N 7.398 13.728 -13.923 -1.680 2.404 0.112 "C2'" C7R 8 C7R "C1'" C5 C 0 1 N N R 7.683 15.162 -14.395 -1.659 1.232 -0.894 "C1'" C7R 9 C7R N1 N1 N 0 1 N N N 8.590 15.938 -13.480 -2.728 0.282 -0.577 N1 C7R 10 C7R C2 C6 C 0 1 N N N 9.562 16.764 -14.039 -2.704 -0.387 0.590 C2 C7R 11 C7R O2 O4 O 0 1 N N N 9.628 16.871 -15.272 -1.790 -0.195 1.374 O2 C7R 12 C7R N3 N2 N 0 1 N N N 10.398 17.436 -13.221 -3.664 -1.256 0.904 N3 C7R 13 C7R C4 C7 C 0 1 N N N 10.300 17.314 -11.908 -4.670 -1.484 0.070 C4 C7R 14 C7R N4 N3 N 0 1 N N N 11.155 18.016 -11.159 -5.655 -2.384 0.405 N4 C7R 15 C7R C5 C8 C 0 1 N N N 9.325 16.464 -11.305 -4.724 -0.800 -1.161 C5 C7R 16 C7R C6 C9 C 0 1 N N N 8.496 15.802 -12.123 -3.744 0.085 -1.464 C6 C7R 17 C7R OP1 O5 O 0 1 N N N 1.464 15.123 -11.470 4.829 0.327 0.419 OP1 C7R 18 C7R SP2 S1 S 0 1 N N N 3.785 14.369 -9.603 3.424 -2.231 0.922 SP2 C7R 19 C7R OP3 O6 O 0 1 N Y N 3.309 16.779 -11.110 4.562 -1.067 -1.668 OP3 C7R 20 C7R "H5'2" H1 H 0 0 N N N 5.666 15.128 -12.036 1.420 0.191 1.105 "H5'2" C7R 21 C7R "H5'1" H2 H 0 0 N N N 4.708 16.456 -12.773 2.372 1.675 0.855 "H5'1" C7R 22 C7R "H4'" H3 H 0 1 N N N 4.537 15.055 -14.851 0.866 2.237 -1.102 "H4'" C7R 23 C7R "H3'" H4 H 0 1 N N N 5.472 12.945 -13.379 -0.296 1.847 1.713 "H3'" C7R 24 C7R H1 H5 H 0 1 N Y N 6.019 12.033 -15.457 -0.239 4.230 1.566 H1 C7R 25 C7R "H2'1" H6 H 0 0 N N N 7.995 13.003 -14.495 -2.450 2.247 0.867 "H2'1" C7R 26 C7R "H2'2" H7 H 0 0 N N N 7.617 13.619 -12.851 -1.841 3.350 -0.406 "H2'2" C7R 27 C7R "H1'" H8 H 0 1 N N N 8.159 15.104 -15.385 -1.787 1.613 -1.907 "H1'" C7R 28 C7R H42 H9 H 0 1 N N N 11.835 18.605 -11.596 -5.616 -2.853 1.253 H42 C7R 29 C7R H41 H10 H 0 1 N N N 11.115 17.952 -10.162 -6.390 -2.549 -0.207 H41 C7R 30 C7R H5 H11 H 0 1 N N N 9.258 16.359 -10.232 -5.536 -0.974 -1.851 H5 C7R 31 C7R H6 H12 H 0 1 N N N 7.742 15.151 -11.704 -3.766 0.625 -2.398 H6 C7R 32 C7R HSP2 H13 H 0 0 N N N 3.084 14.832 -8.611 2.573 -2.938 0.157 HSP2 C7R 33 C7R HOP3 H14 H 0 0 N Y N 2.537 17.296 -11.308 5.382 -1.564 -1.542 HOP3 C7R 34 # # 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 C7R "O3'" "C3'" SING N N 1 C7R O2 C2 DOUB N N 2 C7R "O4'" "C1'" SING N N 3 C7R "O4'" "C4'" SING N N 4 C7R "C1'" "C2'" SING N N 5 C7R "C1'" N1 SING N N 6 C7R "C3'" "C4'" SING N N 7 C7R "C3'" "C2'" SING N N 8 C7R "C4'" "C5'" SING N N 9 C7R C2 N1 SING N N 10 C7R C2 N3 SING N N 11 C7R N1 C6 SING N N 12 C7R N3 C4 DOUB N N 13 C7R "C5'" "O5'" SING N N 14 C7R "O5'" P SING N N 15 C7R C6 C5 DOUB N N 16 C7R C4 C5 SING N N 17 C7R C4 N4 SING N N 18 C7R OP1 P DOUB N N 19 C7R P SP2 SING N N 20 C7R P OP3 SING N N 21 C7R "C5'" "H5'2" SING N N 22 C7R "C5'" "H5'1" SING N N 23 C7R "C4'" "H4'" SING N N 24 C7R "C3'" "H3'" SING N N 25 C7R "O3'" H1 SING N N 26 C7R "C2'" "H2'1" SING N N 27 C7R "C2'" "H2'2" SING N N 28 C7R "C1'" "H1'" SING N N 29 C7R N4 H42 SING N N 30 C7R N4 H41 SING N N 31 C7R C5 H5 SING N N 32 C7R C6 H6 SING N N 33 C7R SP2 HSP2 SING N N 34 C7R OP3 HOP3 SING N N 35 # # 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 C7R SMILES ACDLabs 12.01 "P(S)(O)(OCC1OC(CC1O)N2C=CC(=NC2=O)N)=O" C7R InChI InChI 1.03 "InChI=1S/C9H14N3O6PS/c10-7-1-2-12(9(14)11-7)8-3-5(13)6(18-8)4-17-19(15,16)20/h1-2,5-6,8,13H,3-4H2,(H2,10,11,14)(H2,15,16,20)/t5-,6+,8+/m0/s1" C7R InChIKey InChI 1.03 FHBXKBNKQMSUIJ-SHYZEUOFSA-N C7R SMILES_CANONICAL CACTVS 3.385 "NC1=NC(=O)N(C=C1)[C@H]2C[C@H](O)[C@@H](CO[P](O)(S)=O)O2" C7R SMILES CACTVS 3.385 "NC1=NC(=O)N(C=C1)[CH]2C[CH](O)[CH](CO[P](O)(S)=O)O2" C7R SMILES_CANONICAL "OpenEye OEToolkits" 2.0.4 "C1[C@@H]([C@H](O[C@H]1N2C=CC(=NC2=O)N)COP(=O)(O)S)O" C7R SMILES "OpenEye OEToolkits" 2.0.4 "C1C(C(OC1N2C=CC(=NC2=O)N)COP(=O)(O)S)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 C7R "SYSTEMATIC NAME" ACDLabs 12.01 "2'-deoxy-5'-O-thiophosphonocytidine" C7R "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.4 "[(2~{R},3~{S},5~{R})-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3-oxidanyl-oxolan-2-yl]methoxy-sulfanyl-phosphinic acid" # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site C7R "Create component" 2016-04-28 RCSB C7R "Initial release" 2016-06-22 RCSB C7R "Modify synonyms" 2021-03-01 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id C7R _pdbx_chem_comp_synonyms.name "2'-deoxy-5'-O-thiophosphonocytidine (thiophospho connection isoform 1)" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##