data_GTF # _chem_comp.id GTF _chem_comp.name "2'-deoxy-2',2'-difluorocytidine 5'-(tetrahydrogen triphosphate)" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C9 H14 F2 N3 O13 P3" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms Gemcitabine-TRIPHOSPHATE _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2010-04-12 _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 503.138 _chem_comp.one_letter_code ? _chem_comp.three_letter_code GTF _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 6DW5 _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 GTF F1 F1 F 0 1 N N N -1.180 -0.081 -2.652 -5.424 -1.746 1.484 F1 GTF 1 GTF N1 N1 N 0 1 N N N -3.161 0.808 -0.742 -4.272 1.139 0.501 N1 GTF 2 GTF C2 C1 C 0 1 N N N -3.118 -0.343 0.311 -4.295 1.353 -0.827 C2 GTF 3 GTF F2 F2 F 0 1 N N N -2.860 1.541 -3.292 -5.163 -1.008 -0.677 F2 GTF 4 GTF O2 O1 O 0 1 N N N -2.072 -0.930 0.654 -3.836 0.509 -1.579 O2 GTF 5 GTF N3 N2 N 0 1 N N N -4.459 -0.782 0.890 -4.810 2.471 -1.335 N3 GTF 6 GTF C4 C2 C 0 1 N N N -5.721 -0.088 0.439 -5.316 3.406 -0.540 C4 GTF 7 GTF N4 N3 N 0 1 N N N -6.904 -0.498 1.029 -5.846 4.557 -1.076 N4 GTF 8 GTF C5 C3 C 0 1 N N N -5.793 1.022 -0.569 -5.307 3.212 0.857 C5 GTF 9 GTF C6 C4 C 0 1 N N N -4.487 1.465 -1.164 -4.780 2.070 1.357 C6 GTF 10 GTF PA P1 P 0 1 N N N -3.030 6.733 -1.512 1.662 -1.849 -0.553 PA GTF 11 GTF PB P2 P 0 1 N N N -5.533 7.492 -2.790 4.264 -0.450 -0.313 PB GTF 12 GTF PG P3 P 0 1 N N N -5.857 5.591 -5.270 5.862 1.882 0.579 PG GTF 13 GTF "C1'" C5 C 0 1 N N R -1.791 1.272 -1.247 -3.705 -0.104 1.030 "C1'" GTF 14 GTF O1A O2 O 0 1 N N N -2.054 7.600 -0.604 2.046 -3.409 -0.456 O1A GTF 15 GTF O1B O3 O 0 1 N N N -5.195 8.897 -3.342 4.180 0.088 -1.689 O1B GTF 16 GTF O1G O4 O 0 1 N N N -5.145 4.524 -6.048 5.622 2.952 1.758 O1G GTF 17 GTF "C2'" C6 C 0 1 N N N -1.653 1.218 -2.563 -4.506 -1.321 0.517 "C2'" GTF 18 GTF O2A O5 O 0 1 N N N -2.653 7.293 -2.865 1.541 -1.457 -1.975 O2A GTF 19 GTF O2B O6 O 0 1 N N N -7.019 7.153 -2.385 5.307 -1.675 -0.278 O2B GTF 20 GTF O2G O7 O 0 1 N N N -7.244 5.244 -4.730 7.336 1.251 0.719 O2G GTF 21 GTF "C3'" C7 C 0 1 N N R -0.582 2.316 -2.996 -3.431 -2.405 0.279 "C3'" GTF 22 GTF "O3'" O8 O 0 1 N N N 0.752 2.051 -2.864 -3.671 -3.541 1.111 "O3'" GTF 23 GTF O3A O9 O 0 1 N N N -4.665 7.157 -1.401 2.812 -0.968 0.150 O3A GTF 24 GTF O3B O10 O 0 1 N N N -4.980 6.228 -3.926 4.764 0.709 0.687 O3B GTF 25 GTF O3G O11 O 0 1 N N N -5.888 6.683 -6.305 5.736 2.557 -0.732 O3G GTF 26 GTF "C4'" C8 C 0 1 N N R -1.162 3.541 -2.084 -2.107 -1.714 0.675 "C4'" GTF 27 GTF "O4'" O12 O 0 1 N N N -1.380 2.878 -0.919 -2.368 -0.302 0.521 "O4'" GTF 28 GTF "C5'" C9 C 0 1 N N N -2.454 4.238 -2.704 -0.977 -2.152 -0.259 "C5'" GTF 29 GTF "O5'" O13 O 0 1 N N N -3.135 5.041 -1.730 0.258 -1.594 0.194 "O5'" GTF 30 GTF H1 H1 H 0 1 N N N -6.894 -1.222 1.719 -5.851 4.687 -2.037 H1 GTF 31 GTF H2 H2 H 0 1 N N N -7.769 -0.070 0.766 -6.215 5.238 -0.492 H2 GTF 32 GTF H3 H3 H 0 1 N N N -6.731 1.477 -0.851 -5.714 3.964 1.517 H3 GTF 33 GTF H4 H4 H 0 1 N N N -4.478 2.256 -1.899 -4.762 1.898 2.423 H4 GTF 34 GTF H5 H5 H 0 1 N N N -1.026 0.656 -0.752 -3.697 -0.084 2.119 H5 GTF 35 GTF H6 H6 H 0 1 N N N -1.547 8.186 -1.153 2.142 -3.735 0.449 H6 GTF 36 GTF H7 H7 H 0 1 N N N -4.940 4.848 -6.917 6.249 3.688 1.755 H7 GTF 37 GTF H8 H8 H 0 1 N N N -7.571 7.911 -2.541 5.413 -2.077 0.595 H8 GTF 38 GTF H9 H9 H 0 1 N N N -7.895 5.792 -5.153 7.490 0.792 1.556 H9 GTF 39 GTF H10 H10 H 0 1 N N N -0.804 2.578 -4.041 -3.411 -2.699 -0.771 H10 GTF 40 GTF H11 H11 H 0 1 N N N 1.255 2.799 -3.163 -4.518 -3.978 0.946 H11 GTF 41 GTF H12 H12 H 0 1 N N N -0.370 4.298 -1.984 -1.855 -1.943 1.711 H12 GTF 42 GTF H13 H13 H 0 1 N N N -2.147 4.878 -3.544 -0.906 -3.240 -0.258 H13 GTF 43 GTF H14 H14 H 0 1 N N N -3.140 3.459 -3.069 -1.184 -1.801 -1.270 H14 GTF 44 # # 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 GTF O3G PG DOUB N N 1 GTF O1G PG SING N N 2 GTF PG O2G SING N N 3 GTF PG O3B SING N N 4 GTF O3B PB SING N N 5 GTF O1B PB DOUB N N 6 GTF F2 "C2'" SING N N 7 GTF "C3'" "O3'" SING N N 8 GTF "C3'" "C2'" SING N N 9 GTF "C3'" "C4'" SING N N 10 GTF O2A PA DOUB N N 11 GTF PB O2B SING N N 12 GTF PB O3A SING N N 13 GTF "C5'" "C4'" SING N N 14 GTF "C5'" "O5'" SING N N 15 GTF F1 "C2'" SING N N 16 GTF "C2'" "C1'" SING N N 17 GTF "C4'" "O4'" SING N N 18 GTF "O5'" PA SING N N 19 GTF PA O3A SING N N 20 GTF PA O1A SING N N 21 GTF "C1'" "O4'" SING N N 22 GTF "C1'" N1 SING N N 23 GTF C6 N1 SING N N 24 GTF C6 C5 DOUB N N 25 GTF N1 C2 SING N N 26 GTF C5 C4 SING N N 27 GTF C2 O2 DOUB N N 28 GTF C2 N3 SING N N 29 GTF C4 N3 DOUB N N 30 GTF C4 N4 SING N N 31 GTF N4 H1 SING N N 32 GTF N4 H2 SING N N 33 GTF C5 H3 SING N N 34 GTF C6 H4 SING N N 35 GTF "C1'" H5 SING N N 36 GTF O1A H6 SING N N 37 GTF O1G H7 SING N N 38 GTF O2B H8 SING N N 39 GTF O2G H9 SING N N 40 GTF "C3'" H10 SING N N 41 GTF "O3'" H11 SING N N 42 GTF "C4'" H12 SING N N 43 GTF "C5'" H13 SING N N 44 GTF "C5'" H14 SING N N 45 # # 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 GTF SMILES ACDLabs 12.01 "FC2(F)C(N1C(=O)N=C(N)C=C1)OC(C2O)COP(OP(O)(=O)OP(O)(O)=O)(O)=O" GTF InChI InChI 1.03 "InChI=1S/C9H14F2N3O13P3/c10-9(11)6(15)4(25-7(9)14-2-1-5(12)13-8(14)16)3-24-29(20,21)27-30(22,23)26-28(17,18)19/h1-2,4,6-7,15H,3H2,(H,20,21)(H,22,23)(H2,12,13,16)(H2,17,18,19)/t4-,6-,7-/m1/s1" GTF InChIKey InChI 1.03 YMOXEIOKAJSRQX-QPPQHZFASA-N GTF SMILES_CANONICAL CACTVS 3.385 "NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[C@@H](O)C2(F)F" GTF SMILES CACTVS 3.385 "NC1=NC(=O)N(C=C1)[CH]2O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O)C2(F)F" GTF SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "C1=CN(C(=O)N=C1N)[C@H]2C([C@@H]([C@H](O2)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)(F)F" GTF SMILES "OpenEye OEToolkits" 2.0.6 "C1=CN(C(=O)N=C1N)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)(F)F" # # 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 GTF "SYSTEMATIC NAME" ACDLabs 12.01 "2'-deoxy-2',2'-difluorocytidine 5'-(tetrahydrogen triphosphate)" GTF "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "[[(2~{R},3~{R},5~{R})-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-4,4-bis(fluoranyl)-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen 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 GTF "Create component" 2010-04-12 RCSB GTF "Modify descriptor" 2011-06-04 RCSB GTF "Modify synonyms" 2018-06-27 RCSB GTF "Modify synonyms" 2020-06-05 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id GTF _pdbx_chem_comp_synonyms.name Gemcitabine-TRIPHOSPHATE _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##