data_U7B # _chem_comp.id U7B _chem_comp.name "2'-deoxy-2'2'-difluorodeoxycytidine" _chem_comp.type "DNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C9 H12 F2 N3 O7 P" _chem_comp.mon_nstd_parent_comp_id DC _chem_comp.pdbx_synonyms "[(2~{R},3~{R},5~{R})-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-4,4-bis(fluoranyl)-3-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphite" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2021-01-27 _chem_comp.pdbx_modified_date 2021-04-02 _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 343.178 _chem_comp.one_letter_code C _chem_comp.three_letter_code U7B _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 7NBK _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBE # # 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 U7B P P1 P 0 1 N N N 28.877 23.670 25.673 4.303 1.030 0.022 P U7B 1 U7B "C5'" C1 C 0 1 N N N 26.634 25.071 25.705 2.213 -0.595 -0.338 "C5'" U7B 2 U7B "O5'" O1 O 0 1 N N N 27.455 24.085 26.317 2.949 0.299 0.498 "O5'" U7B 3 U7B "C4'" C2 C 0 1 N N R 25.219 25.131 26.310 0.987 -1.109 0.419 "C4'" U7B 4 U7B "O4'" O2 O 0 1 N N N 24.468 23.932 26.099 0.026 -0.045 0.601 "O4'" U7B 5 U7B "C3'" C3 C 0 1 N N R 25.181 25.417 27.825 0.243 -2.173 -0.418 "C3'" U7B 6 U7B "O3'" O3 O 0 1 N N N 25.334 26.813 28.117 0.606 -3.488 0.007 "O3'" U7B 7 U7B "C2'" C4 C 0 1 N N N 23.813 24.782 28.179 -1.250 -1.903 -0.128 "C2'" U7B 8 U7B "C1'" C5 C 0 1 N N R 23.309 24.050 26.914 -1.233 -0.708 0.851 "C1'" U7B 9 U7B N1 N1 N 0 1 N N N 22.642 22.730 27.186 -2.350 0.197 0.570 N1 U7B 10 U7B C2 C6 C 0 1 N N N 21.271 22.702 27.402 -2.434 0.806 -0.627 C2 U7B 11 U7B O2 O4 O 0 1 N N N 20.584 23.714 27.322 -1.575 0.597 -1.468 O2 U7B 12 U7B N3 N2 N 0 1 N N N 20.643 21.545 27.709 -3.439 1.633 -0.909 N3 U7B 13 U7B C4 C7 C 0 1 N N N 21.356 20.452 27.845 -4.386 1.878 -0.013 C4 U7B 14 U7B N4 N3 N 0 1 N N N 20.694 19.365 28.143 -5.420 2.734 -0.315 N4 U7B 15 U7B C5 C8 C 0 1 N N N 22.755 20.419 27.673 -4.327 1.256 1.252 C5 U7B 16 U7B C6 C9 C 0 1 N N N 23.367 21.584 27.347 -3.302 0.414 1.521 C6 U7B 17 U7B OP1 O5 O 0 1 N N N 29.504 24.890 25.120 4.049 1.770 -1.234 OP1 U7B 18 U7B OP2 O6 O 0 1 N N N 29.624 22.834 26.639 4.787 2.058 1.163 OP2 U7B 19 U7B F1 F1 F 0 1 N N N 22.842 25.706 28.513 -1.842 -3.020 0.472 F1 U7B 20 U7B F2 F2 F 0 1 N N N 24.002 23.893 29.221 -1.925 -1.566 -1.306 F2 U7B 21 U7B "H5''" H1 H 0 0 N N N 26.548 24.840 24.633 1.890 -0.070 -1.237 "H5''" U7B 22 U7B "H5'" H2 H 0 1 N N N 27.112 26.054 25.831 2.846 -1.437 -0.617 "H5'" U7B 23 U7B "H4'" H3 H 0 1 N N N 24.693 25.960 25.814 1.283 -1.523 1.383 "H4'" U7B 24 U7B "H3'" H4 H 0 1 N N N 25.976 24.836 28.315 0.458 -2.043 -1.479 "H3'" U7B 25 U7B H1 H5 H 0 1 N N N 25.305 26.945 29.057 0.169 -4.196 -0.486 H1 U7B 26 U7B "H1'" H6 H 0 1 N N N 22.580 24.707 26.416 -1.279 -1.059 1.882 "H1'" U7B 27 U7B H42 H7 H 0 1 N N N 19.701 19.399 28.254 -5.458 3.160 -1.186 H42 U7B 28 U7B H41 H8 H 0 1 N N N 21.181 18.499 28.260 -6.111 2.911 0.342 H41 U7B 29 U7B H5 H9 H 0 1 N N N 23.316 19.504 27.796 -5.090 1.446 1.992 H5 U7B 30 U7B H6 H10 H 0 1 N N N 24.438 21.606 27.213 -3.237 -0.078 2.480 H6 U7B 31 U7B H3 H12 H 0 1 N N N 30.480 23.217 26.794 5.599 2.535 0.943 H3 U7B 32 U7B OP3 O7 O 0 1 N Y N 28.395 22.735 24.436 5.449 -0.073 -0.227 OP3 U7B 33 U7B H2 H13 H 0 1 N N N 28.612 23.159 23.614 5.667 -0.597 0.555 H2 U7B 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 U7B OP1 P DOUB N N 1 U7B P "O5'" SING N N 2 U7B P OP2 SING N N 3 U7B "C5'" "C4'" SING N N 4 U7B "C5'" "O5'" SING N N 5 U7B "O4'" "C4'" SING N N 6 U7B "O4'" "C1'" SING N N 7 U7B "C4'" "C3'" SING N N 8 U7B "C1'" N1 SING N N 9 U7B "C1'" "C2'" SING N N 10 U7B N1 C6 SING N N 11 U7B N1 C2 SING N N 12 U7B O2 C2 DOUB N N 13 U7B C6 C5 DOUB N N 14 U7B C2 N3 SING N N 15 U7B C5 C4 SING N N 16 U7B N3 C4 DOUB N N 17 U7B "C3'" "O3'" SING N N 18 U7B "C3'" "C2'" SING N N 19 U7B C4 N4 SING N N 20 U7B "C2'" F1 SING N N 21 U7B "C2'" F2 SING N N 22 U7B "C5'" "H5''" SING N N 23 U7B "C5'" "H5'" SING N N 24 U7B "C4'" "H4'" SING N N 25 U7B "C3'" "H3'" SING N N 26 U7B "O3'" H1 SING N N 27 U7B "C1'" "H1'" SING N N 28 U7B N4 H42 SING N N 29 U7B N4 H41 SING N N 30 U7B C5 H5 SING N N 31 U7B C6 H6 SING N N 32 U7B OP2 H3 SING N N 33 U7B P OP3 SING N N 34 U7B OP3 H2 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 U7B InChI InChI 1.03 "InChI=1S/C9H12F2N3O7P/c10-9(11)6(15)4(3-20-22(17,18)19)21-7(9)14-2-1-5(12)13-8(14)16/h1-2,4,6-7,15H,3H2,(H2,12,13,16)(H2,17,18,19)/t4-,6-,7-/m1/s1" U7B InChIKey InChI 1.03 KNTREFQOVSMROS-QPPQHZFASA-N U7B SMILES_CANONICAL CACTVS 3.385 "NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO[P](O)(O)=O)[C@@H](O)C2(F)F" U7B SMILES CACTVS 3.385 "NC1=NC(=O)N(C=C1)[CH]2O[CH](CO[P](O)(O)=O)[CH](O)C2(F)F" U7B SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C1=CN(C(=O)N=C1N)[C@H]2C([C@@H]([C@H](O2)COP(=O)(O)O)O)(F)F" U7B SMILES "OpenEye OEToolkits" 2.0.7 "C1=CN(C(=O)N=C1N)C2C(C(C(O2)COP(=O)(O)O)O)(F)F" # _pdbx_chem_comp_identifier.comp_id U7B _pdbx_chem_comp_identifier.type "SYSTEMATIC NAME" _pdbx_chem_comp_identifier.program "OpenEye OEToolkits" _pdbx_chem_comp_identifier.program_version 2.0.7 _pdbx_chem_comp_identifier.identifier "[(2~{R},3~{R},5~{R})-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-4,4-bis(fluoranyl)-3-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphate" # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id U7B _pdbx_chem_comp_synonyms.name "[(2~{R},3~{R},5~{R})-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-4,4-bis(fluoranyl)-3-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphite" _pdbx_chem_comp_synonyms.provenance PDB _pdbx_chem_comp_synonyms.type ? # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site U7B "Create component" 2021-01-27 PDBE U7B "Modify synonyms" 2021-03-13 RCSB U7B "Initial release" 2021-04-07 RCSB ##