data_5BT # _chem_comp.id 5BT _chem_comp.name "5-bromo-2'-deoxycytidine" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C9 H12 Br N3 O4" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "5-bromo-2'-doxy-D-cytidine" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2011-01-25 _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 306.113 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 5BT _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 3QEN _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 5BT N1 N1 N 0 1 N N N -12.529 27.938 -22.559 0.193 0.008 -0.153 N1 5BT 1 5BT C2 C2 C 0 1 N N N -11.129 28.115 -22.503 0.177 1.312 -0.486 C2 5BT 2 5BT O2 O2 O 0 1 N N N -10.656 29.271 -22.553 1.229 1.887 -0.712 O2 5BT 3 5BT N3 N3 N 0 1 N N N -10.285 27.083 -22.430 -0.969 1.984 -0.575 N3 5BT 4 5BT C4 C4 C 0 1 N N N -10.717 25.821 -22.389 -2.128 1.384 -0.336 C4 5BT 5 5BT N4 N4 N 0 1 N N N -9.785 24.829 -22.320 -3.305 2.089 -0.431 N4 5BT 6 5BT C5 C5 C 0 1 N N N -12.191 25.599 -22.425 -2.146 0.018 0.017 C5 5BT 7 5BT BR5 BR5 BR 0 0 N N N -13.040 23.890 -22.392 -3.783 -0.863 0.363 BR5 5BT 8 5BT C6 C6 C 0 1 N N N -13.030 26.707 -22.503 -0.972 -0.652 0.103 C6 5BT 9 5BT "C1'" "C1'" C 0 1 N N R -13.408 29.127 -22.580 1.469 -0.706 -0.069 "C1'" 5BT 10 5BT "C2'" "C2'" C 0 1 N N N -14.185 29.460 -23.853 2.176 -0.708 -1.443 "C2'" 5BT 11 5BT "C3'" "C3'" C 0 1 N N S -15.555 29.862 -23.326 3.674 -0.555 -1.095 "C3'" 5BT 12 5BT "O3'" "O3'" O 0 1 N N N -15.575 31.262 -22.987 4.412 -1.691 -1.551 "O3'" 5BT 13 5BT "C4'" "C4'" C 0 1 N N R -15.712 29.094 -22.032 3.695 -0.480 0.448 "C4'" 5BT 14 5BT "O4'" "O4'" O 0 1 N N N -14.379 28.987 -21.519 2.378 -0.012 0.812 "O4'" 5BT 15 5BT "C5'" "C5'" C 0 1 N N N -16.337 27.714 -22.270 4.761 0.511 0.918 "C5'" 5BT 16 5BT "O5'" "O5'" O 0 1 N N N -17.551 27.662 -21.515 4.845 0.480 2.344 "O5'" 5BT 17 5BT HN4 HN4 H 0 1 N N N -8.812 25.058 -22.302 -3.290 3.028 -0.674 HN4 5BT 18 5BT HN4A HN4A H 0 0 N N N -10.074 23.872 -22.288 -4.151 1.648 -0.255 HN4A 5BT 19 5BT H6 H6 H 0 1 N N N -14.101 26.566 -22.518 -0.959 -1.698 0.370 H6 5BT 20 5BT "H1'" "H1'" H 0 1 N N N -12.695 29.958 -22.477 1.310 -1.727 0.278 "H1'" 5BT 21 5BT "H2'" "H2'" H 0 1 N N N -13.711 30.278 -24.416 1.998 -1.649 -1.963 "H2'" 5BT 22 5BT "H2'A" "H2'A" H 0 0 N N N -14.248 28.594 -24.528 1.837 0.133 -2.048 "H2'A" 5BT 23 5BT "H3'" "H3'" H 0 1 N N N -16.339 29.662 -24.071 4.075 0.360 -1.530 "H3'" 5BT 24 5BT "HO3'" "HO3'" H 0 0 N N N -16.436 31.497 -22.660 4.382 -1.821 -2.509 "HO3'" 5BT 25 5BT "H4'" "H4'" H 0 1 N N N -16.389 29.599 -21.327 3.878 -1.466 0.873 "H4'" 5BT 26 5BT "H5'" "H5'" H 0 1 N N N -16.548 27.572 -23.340 5.726 0.236 0.491 "H5'" 5BT 27 5BT "H5'A" "H5'A" H 0 0 N N N -15.649 26.923 -21.938 4.493 1.516 0.591 "H5'A" 5BT 28 5BT "HO5'" "HO5'" H 0 0 N N N -17.966 26.817 -21.640 5.503 1.085 2.713 "HO5'" 5BT 29 # # 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 5BT "C1'" N1 SING N N 1 5BT N1 C6 SING N N 2 5BT N1 C2 SING N N 3 5BT O2 C2 DOUB N N 4 5BT C2 N3 SING N N 5 5BT N3 C4 DOUB N N 6 5BT C5 C4 SING N N 7 5BT C4 N4 SING N N 8 5BT N4 HN4 SING N N 9 5BT N4 HN4A SING N N 10 5BT C6 C5 DOUB N N 11 5BT C5 BR5 SING N N 12 5BT C6 H6 SING N N 13 5BT "C2'" "C1'" SING N N 14 5BT "C1'" "O4'" SING N N 15 5BT "C1'" "H1'" SING N N 16 5BT "C2'" "C3'" SING N N 17 5BT "C2'" "H2'" SING N N 18 5BT "C2'" "H2'A" SING N N 19 5BT "C3'" "O3'" SING N N 20 5BT "C3'" "C4'" SING N N 21 5BT "C3'" "H3'" SING N N 22 5BT "O3'" "HO3'" SING N N 23 5BT "C5'" "C4'" SING N N 24 5BT "C4'" "O4'" SING N N 25 5BT "C4'" "H4'" SING N N 26 5BT "C5'" "O5'" SING N N 27 5BT "C5'" "H5'" SING N N 28 5BT "C5'" "H5'A" SING N N 29 5BT "O5'" "HO5'" SING N N 30 # # 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 5BT SMILES ACDLabs 12.01 "BrC=1C(=NC(=O)N(C=1)C2OC(C(O)C2)CO)N" 5BT SMILES_CANONICAL CACTVS 3.370 "NC1=NC(=O)N(C=C1Br)[C@H]2C[C@H](O)[C@@H](CO)O2" 5BT SMILES CACTVS 3.370 "NC1=NC(=O)N(C=C1Br)[CH]2C[CH](O)[CH](CO)O2" 5BT SMILES_CANONICAL "OpenEye OEToolkits" 1.7.0 "C1[C@@H]([C@H](O[C@H]1N2C=C(C(=NC2=O)N)Br)CO)O" 5BT SMILES "OpenEye OEToolkits" 1.7.0 "C1C(C(OC1N2C=C(C(=NC2=O)N)Br)CO)O" 5BT InChI InChI 1.03 "InChI=1S/C9H12BrN3O4/c10-4-2-13(9(16)12-8(4)11)7-1-5(15)6(3-14)17-7/h2,5-7,14-15H,1,3H2,(H2,11,12,16)/t5-,6+,7+/m0/s1" 5BT InChIKey InChI 1.03 KISUPFXQEHWGAR-RRKCRQDMSA-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 5BT "SYSTEMATIC NAME" ACDLabs 12.01 "5-bromo-2'-deoxycytidine" 5BT "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.0 "4-azanyl-5-bromo-1-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]pyrimidin-2-one" # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site 5BT "Create component" 2011-01-25 RCSB 5BT "Modify descriptor" 2011-06-04 RCSB 5BT "Modify synonyms" 2020-06-05 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id 5BT _pdbx_chem_comp_synonyms.name "5-bromo-2'-doxy-D-cytidine" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##