data_4U3 # _chem_comp.id 4U3 _chem_comp.name "5-chloro-2'-deoxycytidine 5'-(dihydrogen phosphate)" _chem_comp.type "DNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C9 H13 Cl N3 O7 P" _chem_comp.mon_nstd_parent_comp_id DC _chem_comp.pdbx_synonyms "5-Chloro-5'-deoxycytidine" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2015-05-27 _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 341.642 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 4U3 _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 5BOM _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 4U3 C2 C1 C 0 1 N N N -1.903 -11.576 16.246 -1.970 0.118 -1.148 C2 4U3 1 4U3 N3 N1 N 0 1 N N N -0.657 -10.908 16.438 -3.015 0.815 -1.591 N3 4U3 2 4U3 C4 C2 C 0 1 N N N -0.326 -10.346 17.712 -4.080 1.001 -0.823 C4 4U3 3 4U3 C5 C3 C 0 1 N N N -1.256 -10.465 18.791 -4.105 0.455 0.478 C5 4U3 4 4U3 C6 C4 C 0 1 N N N -2.507 -11.119 18.596 -3.035 -0.252 0.914 C6 4U3 5 4U3 CL5 CL1 CL 0 0 N N N -0.840 -9.770 20.308 -5.487 0.685 1.503 CL5 4U3 6 4U3 P P1 P 0 1 N N N -5.308 -9.340 20.599 4.589 1.102 0.201 P 4U3 7 4U3 OP1 O1 O 0 1 N N N -4.315 -10.191 21.461 5.707 0.175 -0.082 OP1 4U3 8 4U3 OP2 O2 O 0 1 N N N -4.763 -7.975 20.165 4.296 2.003 -1.101 OP2 4U3 9 4U3 "C5'" C5 C 0 1 N N N -6.506 -11.155 19.197 2.730 -0.757 -0.272 "C5'" 4U3 10 4U3 "O5'" O3 O 0 1 N N N -5.662 -10.076 19.298 3.272 0.257 0.577 "O5'" 4U3 11 4U3 "C4'" C6 C 0 1 N N R -6.259 -11.900 17.896 1.484 -1.358 0.382 "C4'" 4U3 12 4U3 "O4'" O4 O 0 1 N N N -5.175 -11.371 17.154 0.406 -0.397 0.389 "O4'" 4U3 13 4U3 "C3'" C7 C 0 1 N N S -5.931 -13.293 18.239 0.953 -2.541 -0.457 "C3'" 4U3 14 4U3 "O3'" O5 O 0 1 N N N -6.592 -14.097 17.363 1.400 -3.784 0.090 "O3'" 4U3 15 4U3 "C2'" C8 C 0 1 N N N -4.446 -13.395 18.163 -0.583 -2.420 -0.348 "C2'" 4U3 16 4U3 "C1'" C9 C 0 1 N N R -4.140 -12.340 17.154 -0.799 -1.178 0.545 "C1'" 4U3 17 4U3 N1 N2 N 0 1 N N N -2.838 -11.678 17.326 -1.963 -0.416 0.087 N1 4U3 18 4U3 O2 O6 O 0 1 N N N -2.183 -12.103 15.000 -1.004 -0.043 -1.877 O2 4U3 19 4U3 N4 N3 N 0 1 N N N 0.943 -9.679 17.885 -5.153 1.724 -1.291 N4 4U3 20 4U3 H6 H1 H 0 1 N N N -3.208 -11.192 19.414 -3.030 -0.680 1.905 H6 4U3 21 4U3 HOP2 H3 H 0 0 N N N -3.881 -7.864 20.501 3.573 2.635 -0.987 HOP2 4U3 22 4U3 "H5''" H4 H 0 0 N N N -7.548 -10.804 19.221 2.460 -0.321 -1.234 "H5''" 4U3 23 4U3 "H5'" H5 H 0 1 N N N -6.328 -11.835 20.043 3.473 -1.540 -0.424 "H5'" 4U3 24 4U3 "H4'" H6 H 0 1 N N N -7.179 -11.878 17.294 1.709 -1.684 1.398 "H4'" 4U3 25 4U3 H7 H7 H 0 1 N N N -6.250 -13.495 19.272 1.271 -2.446 -1.495 H7 4U3 26 4U3 "HO3'" H8 H 0 0 N N N -6.399 -15.006 17.560 1.095 -4.561 -0.399 "HO3'" 4U3 27 4U3 "H2'" H9 H 0 1 N N N -4.126 -14.389 17.818 -1.025 -2.264 -1.332 "H2'" 4U3 28 4U3 "H2''" H10 H 0 0 N N N -3.976 -13.175 19.133 -1.004 -3.309 0.123 "H2''" 4U3 29 4U3 "H1'" H11 H 0 1 N N N -4.132 -12.828 16.168 -0.926 -1.474 1.586 "H1'" 4U3 30 4U3 H41 H12 H 0 1 N N N 1.582 -9.613 17.118 -5.132 2.098 -2.185 H41 4U3 31 4U3 H42 H13 H 0 1 N N N 1.183 -9.283 18.771 -5.930 1.858 -0.727 H42 4U3 32 4U3 OP3 O3P O 0 1 N Y N -6.715 -9.185 21.367 4.984 2.057 1.436 OP3 4U3 33 4U3 HOP3 H2 H 0 0 N Y N -6.674 -9.641 22.199 5.770 2.597 1.280 HOP3 4U3 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 4U3 O2 C2 DOUB N N 1 4U3 C2 N3 SING N N 2 4U3 C2 N1 SING N N 3 4U3 N3 C4 DOUB N N 4 4U3 "C1'" "O4'" SING N N 5 4U3 "C1'" N1 SING N N 6 4U3 "C1'" "C2'" SING N N 7 4U3 "O4'" "C4'" SING N N 8 4U3 N1 C6 SING N N 9 4U3 "O3'" "C3'" SING N N 10 4U3 C4 N4 SING N N 11 4U3 C4 C5 SING N N 12 4U3 "C4'" "C3'" SING N N 13 4U3 "C4'" "C5'" SING N N 14 4U3 "C2'" "C3'" SING N N 15 4U3 C6 C5 DOUB N N 16 4U3 C5 CL5 SING N N 17 4U3 "C5'" "O5'" SING N N 18 4U3 "O5'" P SING N N 19 4U3 OP2 P SING N N 20 4U3 P OP1 DOUB N N 21 4U3 C6 H6 SING N N 22 4U3 OP2 HOP2 SING N N 23 4U3 "C5'" "H5''" SING N N 24 4U3 "C5'" "H5'" SING N N 25 4U3 "C4'" "H4'" SING N N 26 4U3 "C3'" H7 SING N N 27 4U3 "O3'" "HO3'" SING N N 28 4U3 "C2'" "H2'" SING N N 29 4U3 "C2'" "H2''" SING N N 30 4U3 "C1'" "H1'" SING N N 31 4U3 N4 H41 SING N N 32 4U3 N4 H42 SING N N 33 4U3 P OP3 SING N N 34 4U3 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 4U3 SMILES ACDLabs 12.01 "C1(N=C(N)C(Cl)=CN1C2OC(COP(=O)(O)O)C(O)C2)=O" 4U3 InChI InChI 1.03 "InChI=1S/C9H13ClN3O7P/c10-4-2-13(9(15)12-8(4)11)7-1-5(14)6(20-7)3-19-21(16,17)18/h2,5-7,14H,1,3H2,(H2,11,12,15)(H2,16,17,18)/t5-,6+,7+/m0/s1" 4U3 InChIKey InChI 1.03 JXVVNBLPBHXIAA-RRKCRQDMSA-N 4U3 SMILES_CANONICAL CACTVS 3.385 "NC1=NC(=O)N(C=C1Cl)[C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=O)O2" 4U3 SMILES CACTVS 3.385 "NC1=NC(=O)N(C=C1Cl)[CH]2C[CH](O)[CH](CO[P](O)(O)=O)O2" 4U3 SMILES_CANONICAL "OpenEye OEToolkits" 1.9.2 "C1[C@@H]([C@H](O[C@H]1N2C=C(C(=NC2=O)N)Cl)COP(=O)(O)O)O" 4U3 SMILES "OpenEye OEToolkits" 1.9.2 "C1C(C(OC1N2C=C(C(=NC2=O)N)Cl)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 4U3 "SYSTEMATIC NAME" ACDLabs 12.01 "5-chloro-2'-deoxycytidine 5'-(dihydrogen phosphate)" 4U3 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.9.2 "[(2R,3S,5R)-5-(4-azanyl-5-chloranyl-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 4U3 "Create component" 2015-05-27 RCSB 4U3 "Initial release" 2015-08-19 RCSB 4U3 "Modify synonyms" 2020-06-05 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id 4U3 _pdbx_chem_comp_synonyms.name "5-Chloro-5'-deoxycytidine" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##